Forgot to remove the beta designation before creating html and man pages.

Fixed a bug in the altivec detection due to inlining optimization.

diff --git a/include/copyrite.h b/include/copyrite.h
index 56c141e4ebdc0331f599faac173a2b5d234fcde8..e5d35de0a4aca3a147a57352453fd2f665257f81 100644 (file)
--- a/include/copyrite.h
+++ b/include/copyrite.h
@@ -53,7 +53,7 @@ char *GromacsVersion(void);
   
   
 static char *CopyrightText[] = {
-  "Copyright (c) 1991-2001, University of Groningen, The Netherlands"
+  "Copyright (c) 1991-2002, University of Groningen, The Netherlands"
 };
 
 static char *GPLText[] = {

diff --git a/man/man1/do_dssp.1 b/man/man1/do_dssp.1
index 141889a51206a5d36060f3e43e5f2d763263ef5a..c75eee0a20712d5177ad12c44e7694760991c3fe 100644 (file)
--- a/man/man1/do_dssp.1
+++ b/man/man1/do_dssp.1
@@ -1,7 +1,7 @@
-.TH do_dssp 1 "Wed 27 Feb 2002"
+.TH do_dssp 1 "Thu 28 Feb 2002"
 .SH NAME
 do_dssp
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3do_dssp\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/editconf.1 b/man/man1/editconf.1
index 1268979c10843002a621cf48d3836894f9b5bc68..a13fb07557576785adf4f20231d6dc517e7fea81 100644 (file)
--- a/man/man1/editconf.1
+++ b/man/man1/editconf.1
@@ -1,7 +1,7 @@
-.TH editconf 1 "Wed 27 Feb 2002"
+.TH editconf 1 "Thu 28 Feb 2002"
 .SH NAME
 editconf
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3editconf\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/eneconv.1 b/man/man1/eneconv.1
index c5baec53e9ee1517faa7844ae066a17294156f29..5217f8fe6429fc793ed5cf8b3a5288148e4c9fce 100644 (file)
--- a/man/man1/eneconv.1
+++ b/man/man1/eneconv.1
@@ -1,7 +1,7 @@
-.TH eneconv 1 "Wed 27 Feb 2002"
+.TH eneconv 1 "Thu 28 Feb 2002"
 .SH NAME
 eneconv
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3eneconv\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_anaeig.1 b/man/man1/g_anaeig.1
index e846b0fccdfb43aef074af8a3ccb978c85fac74e..219833282348cbb15a49ff01483f56e429acc33a 100644 (file)
--- a/man/man1/g_anaeig.1
+++ b/man/man1/g_anaeig.1
@@ -1,7 +1,7 @@
-.TH g_anaeig 1 "Wed 27 Feb 2002"
+.TH g_anaeig 1 "Thu 28 Feb 2002"
 .SH NAME
 g_anaeig
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_anaeig\fP
 .BI "-v" " eigenvec.trr "

diff --git a/man/man1/g_analyze.1 b/man/man1/g_analyze.1
index 57009351103f2dcd4b12cee8737cc4497ce07ffa..e75f36013cc9fde2196931ca8b394bc87d0d58e4 100644 (file)
--- a/man/man1/g_analyze.1
+++ b/man/man1/g_analyze.1
@@ -1,7 +1,7 @@
-.TH g_analyze 1 "Wed 27 Feb 2002"
+.TH g_analyze 1 "Thu 28 Feb 2002"
 .SH NAME
 g_analyze
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_analyze\fP
 .BI "-f" " graph.xvg "

diff --git a/man/man1/g_angle.1 b/man/man1/g_angle.1
index 06358e551a23e0991ea49ca7448a45b57a8e10af..bc73855e1e73f9d298d75148d34a564f09951e43 100644 (file)
--- a/man/man1/g_angle.1
+++ b/man/man1/g_angle.1
@@ -1,7 +1,7 @@
-.TH g_angle 1 "Wed 27 Feb 2002"
+.TH g_angle 1 "Thu 28 Feb 2002"
 .SH NAME
 g_angle
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_angle\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_bond.1 b/man/man1/g_bond.1
index 3840cf8563dfc87776b701f42d5a43333c90e703..e51e837a835c585ae11b955c362ae54f4ff35da6 100644 (file)
--- a/man/man1/g_bond.1
+++ b/man/man1/g_bond.1
@@ -1,7 +1,7 @@
-.TH g_bond 1 "Wed 27 Feb 2002"
+.TH g_bond 1 "Thu 28 Feb 2002"
 .SH NAME
 g_bond
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_bond\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_bundle.1 b/man/man1/g_bundle.1
index de792f2b16c0f75c578cf9e601fbfdb3ca63a1d8..03b569e41c1f85c4f71171e70d1587adfb08c39b 100644 (file)
--- a/man/man1/g_bundle.1
+++ b/man/man1/g_bundle.1
@@ -1,7 +1,7 @@
-.TH g_bundle 1 "Wed 27 Feb 2002"
+.TH g_bundle 1 "Thu 28 Feb 2002"
 .SH NAME
 g_bundle
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_bundle\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_chi.1 b/man/man1/g_chi.1
index 503a7278fc1d7310d2689b4046617a9a322631c8..b3d8f070cde23f04f5ac1de3b9a2dddd76018d5e 100644 (file)
--- a/man/man1/g_chi.1
+++ b/man/man1/g_chi.1
@@ -1,7 +1,7 @@
-.TH g_chi 1 "Wed 27 Feb 2002"
+.TH g_chi 1 "Thu 28 Feb 2002"
 .SH NAME
 g_chi
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_chi\fP
 .BI "-c" " conf.gro "

diff --git a/man/man1/g_cluster.1 b/man/man1/g_cluster.1
index 7c83d377b17718c4b9dc5c5d37e7e742bb80344e..912df1fdd8b7316aac363163d894269089b7a369 100644 (file)
--- a/man/man1/g_cluster.1
+++ b/man/man1/g_cluster.1
@@ -1,7 +1,7 @@
-.TH g_cluster 1 "Wed 27 Feb 2002"
+.TH g_cluster 1 "Thu 28 Feb 2002"
 .SH NAME
 g_cluster
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_cluster\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_confrms.1 b/man/man1/g_confrms.1
index f3b521f82a2e72561f8ff76561596c665a9d01f5..09e542bc4527e4fe29ad946d133aaa937e0442f3 100644 (file)
--- a/man/man1/g_confrms.1
+++ b/man/man1/g_confrms.1
@@ -1,7 +1,7 @@
-.TH g_confrms 1 "Wed 27 Feb 2002"
+.TH g_confrms 1 "Thu 28 Feb 2002"
 .SH NAME
 g_confrms
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_confrms\fP
 .BI "-f1" " conf1.gro "

diff --git a/man/man1/g_covar.1 b/man/man1/g_covar.1
index b7b4d5d0cd8b0d732e46743df6855afbe56edf30..ee585772d72a51b1f38d646f0259896677e9ab1d 100644 (file)
--- a/man/man1/g_covar.1
+++ b/man/man1/g_covar.1
@@ -1,7 +1,7 @@
-.TH g_covar 1 "Wed 27 Feb 2002"
+.TH g_covar 1 "Thu 28 Feb 2002"
 .SH NAME
 g_covar
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_covar\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_density.1 b/man/man1/g_density.1
index e63e618bc53a72183553e532f9b6385fffa1f57c..ac1bb5411bab6a1998a433621aea6d3984727a22 100644 (file)
--- a/man/man1/g_density.1
+++ b/man/man1/g_density.1
@@ -1,7 +1,7 @@
-.TH g_density 1 "Wed 27 Feb 2002"
+.TH g_density 1 "Thu 28 Feb 2002"
 .SH NAME
 g_density
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_density\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_dielectric.1 b/man/man1/g_dielectric.1
index 9940d2cf5228f907ec0bc89703d638c90ff6bbbb..dbae1b73ba9adc522c28666afe66e33884f40e8c 100644 (file)
--- a/man/man1/g_dielectric.1
+++ b/man/man1/g_dielectric.1
@@ -1,7 +1,7 @@
-.TH g_dielectric 1 "Wed 27 Feb 2002"
+.TH g_dielectric 1 "Thu 28 Feb 2002"
 .SH NAME
 g_dielectric
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_dielectric\fP
 .BI "-f" " Mtot.xvg "

diff --git a/man/man1/g_dih.1 b/man/man1/g_dih.1
index 073b2e459382a2377b562ecd8ad778ff78fdc5cb..41683f4cfb7e1090921b436b6ba71f5b9c619256 100644 (file)
--- a/man/man1/g_dih.1
+++ b/man/man1/g_dih.1
@@ -1,7 +1,7 @@
-.TH g_dih 1 "Wed 27 Feb 2002"
+.TH g_dih 1 "Thu 28 Feb 2002"
 .SH NAME
 g_dih
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_dih\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_dipoles.1 b/man/man1/g_dipoles.1
index df3dc031ee9533d60be587fb4494ba62eb5e4e8b..77ac6f2800d21b2f99e70f118bc818c8a16378a5 100644 (file)
--- a/man/man1/g_dipoles.1
+++ b/man/man1/g_dipoles.1
@@ -1,7 +1,7 @@
-.TH g_dipoles 1 "Wed 27 Feb 2002"
+.TH g_dipoles 1 "Thu 28 Feb 2002"
 .SH NAME
 g_dipoles
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_dipoles\fP
 .BI "-enx" " ener.edr "

diff --git a/man/man1/g_disre.1 b/man/man1/g_disre.1
index e993e16140d774635cdb0be65cb8d623864cc2f2..dd24bc270c8c85354dedefb1ddb603d937961094 100644 (file)
--- a/man/man1/g_disre.1
+++ b/man/man1/g_disre.1
@@ -1,7 +1,7 @@
-.TH g_disre 1 "Wed 27 Feb 2002"
+.TH g_disre 1 "Thu 28 Feb 2002"
 .SH NAME
 g_disre
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_disre\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/g_dist.1 b/man/man1/g_dist.1
index ebf3bc63a441481147d3c09db035d952562793f6..5694f8b655efeea3ea842e7bba46ffb6f768b629 100644 (file)
--- a/man/man1/g_dist.1
+++ b/man/man1/g_dist.1
@@ -1,7 +1,7 @@
-.TH g_dist 1 "Wed 27 Feb 2002"
+.TH g_dist 1 "Thu 28 Feb 2002"
 .SH NAME
 g_dist
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_dist\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_dyndom.1 b/man/man1/g_dyndom.1
index aa7a6c83724834e3488f54dd6e977cdc1c054c58..73c75cf62d5d219971c2b79c5f33c921cb2b6a7f 100644 (file)
--- a/man/man1/g_dyndom.1
+++ b/man/man1/g_dyndom.1
@@ -1,7 +1,7 @@
-.TH g_dyndom 1 "Wed 27 Feb 2002"
+.TH g_dyndom 1 "Thu 28 Feb 2002"
 .SH NAME
 g_dyndom
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_dyndom\fP
 .BI "-f" " dyndom.pdb "

diff --git a/man/man1/g_enemat.1 b/man/man1/g_enemat.1
index e1c50468e36da2ba4306467df1c438143256bd2d..69a81a4b19402b3f78d377cb167426320998ee6e 100644 (file)
--- a/man/man1/g_enemat.1
+++ b/man/man1/g_enemat.1
@@ -1,7 +1,7 @@
-.TH g_enemat 1 "Wed 27 Feb 2002"
+.TH g_enemat 1 "Thu 28 Feb 2002"
 .SH NAME
 g_enemat
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_enemat\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_energy.1 b/man/man1/g_energy.1
index 1a75340e133e5d0d720e7a246a487d343083b5d0..8ea465a41eac9cad467d9ac6663f909614d1cc6f 100644 (file)
--- a/man/man1/g_energy.1
+++ b/man/man1/g_energy.1
@@ -1,7 +1,7 @@
-.TH g_energy 1 "Wed 27 Feb 2002"
+.TH g_energy 1 "Thu 28 Feb 2002"
 .SH NAME
 g_energy
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_energy\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_gyrate.1 b/man/man1/g_gyrate.1
index 6326e34207a288b974d4ea7af4353eef018f2e44..eda2497cab4ba5fffe758e90a4ea3039c1cdc1f3 100644 (file)
--- a/man/man1/g_gyrate.1
+++ b/man/man1/g_gyrate.1
@@ -1,7 +1,7 @@
-.TH g_gyrate 1 "Wed 27 Feb 2002"
+.TH g_gyrate 1 "Thu 28 Feb 2002"
 .SH NAME
 g_gyrate
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_gyrate\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_h2order.1 b/man/man1/g_h2order.1
index 62a1ecfce8e06085dafc6b7bb525dc008d2b3b07..ed35671234574b60f1aa329b3e4e2899355a0b25 100644 (file)
--- a/man/man1/g_h2order.1
+++ b/man/man1/g_h2order.1
@@ -1,7 +1,7 @@
-.TH g_h2order 1 "Wed 27 Feb 2002"
+.TH g_h2order 1 "Thu 28 Feb 2002"
 .SH NAME
 g_h2order
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_h2order\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_hbond.1 b/man/man1/g_hbond.1
index c908a10982ce30ae742d73bea7eb857dc0f4c645..6cf532047241282166a153c8c950e37dea1357ac 100644 (file)
--- a/man/man1/g_hbond.1
+++ b/man/man1/g_hbond.1
@@ -1,7 +1,7 @@
-.TH g_hbond 1 "Wed 27 Feb 2002"
+.TH g_hbond 1 "Thu 28 Feb 2002"
 .SH NAME
 g_hbond
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_hbond\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_helix.1 b/man/man1/g_helix.1
index 3b9ccb8a701964d7734008407188e53009329481..7e2cf62d817c95bd15633ccfd85c93a7d0000997 100644 (file)
--- a/man/man1/g_helix.1
+++ b/man/man1/g_helix.1
@@ -1,7 +1,7 @@
-.TH g_helix 1 "Wed 27 Feb 2002"
+.TH g_helix 1 "Thu 28 Feb 2002"
 .SH NAME
 g_helix
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_helix\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/g_lie.1 b/man/man1/g_lie.1
index bda330c1c06cf798a570b62f9446d8abac3eb4b6..3aacb7c7ab674974be434a4316d4382d190909d0 100644 (file)
--- a/man/man1/g_lie.1
+++ b/man/man1/g_lie.1
@@ -1,7 +1,7 @@
-.TH g_lie 1 "Wed 27 Feb 2002"
+.TH g_lie 1 "Thu 28 Feb 2002"
 .SH NAME
 g_lie
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_lie\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_mdmat.1 b/man/man1/g_mdmat.1
index 947d2c43c842adfaae991beb1525141cfe421a9d..3d43f0b616c6713df3892bfc1c11372558c8db8d 100644 (file)
--- a/man/man1/g_mdmat.1
+++ b/man/man1/g_mdmat.1
@@ -1,7 +1,7 @@
-.TH g_mdmat 1 "Wed 27 Feb 2002"
+.TH g_mdmat 1 "Thu 28 Feb 2002"
 .SH NAME
 g_mdmat
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_mdmat\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_mindist.1 b/man/man1/g_mindist.1
index ae76dfad517cd60337191a3971f9ecfec5900233..cc70d05e5f10e9c81a45876d49457b0d1d4dd8e8 100644 (file)
--- a/man/man1/g_mindist.1
+++ b/man/man1/g_mindist.1
@@ -1,7 +1,7 @@
-.TH g_mindist 1 "Wed 27 Feb 2002"
+.TH g_mindist 1 "Thu 28 Feb 2002"
 .SH NAME
 g_mindist
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_mindist\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_morph.1 b/man/man1/g_morph.1
index 18a51df00f5c3e5b448eb1cb2e7a357b5c97547b..25d9c6892a1680cebc8560e24bbc87d1e4472938 100644 (file)
--- a/man/man1/g_morph.1
+++ b/man/man1/g_morph.1
@@ -1,7 +1,7 @@
-.TH g_morph 1 "Wed 27 Feb 2002"
+.TH g_morph 1 "Thu 28 Feb 2002"
 .SH NAME
 g_morph
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_morph\fP
 .BI "-f1" " conf1.gro "

diff --git a/man/man1/g_msd.1 b/man/man1/g_msd.1
index 0589bce1f7c292c2a4a98ec762e14c7cc0932c29..5055d311e04bd252dcd2c922360d47d878b7ee22 100644 (file)
--- a/man/man1/g_msd.1
+++ b/man/man1/g_msd.1
@@ -1,7 +1,7 @@
-.TH g_msd 1 "Wed 27 Feb 2002"
+.TH g_msd 1 "Thu 28 Feb 2002"
 .SH NAME
 g_msd
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_msd\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_nmeig.1 b/man/man1/g_nmeig.1
index 5ea15bb047edbf1379e6c65752c2c113cae0cdd4..c6602c555f6c3574e45beb7af5f4406c0d813efa 100644 (file)
--- a/man/man1/g_nmeig.1
+++ b/man/man1/g_nmeig.1
@@ -1,7 +1,7 @@
-.TH g_nmeig 1 "Wed 27 Feb 2002"
+.TH g_nmeig 1 "Thu 28 Feb 2002"
 .SH NAME
 g_nmeig
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_nmeig\fP
 .BI "-f" " hessian.mtx "

diff --git a/man/man1/g_nmens.1 b/man/man1/g_nmens.1
index 1811df1b91fb82c422eefcc0f6b52f65ecd18448..e9d40c02f33504b7d0ba49c98866c1f8f6fade63 100644 (file)
--- a/man/man1/g_nmens.1
+++ b/man/man1/g_nmens.1
@@ -1,7 +1,7 @@
-.TH g_nmens 1 "Wed 27 Feb 2002"
+.TH g_nmens 1 "Thu 28 Feb 2002"
 .SH NAME
 g_nmens
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_nmens\fP
 .BI "-v" " eigenvec.trr "

diff --git a/man/man1/g_order.1 b/man/man1/g_order.1
index 1b44e00a2a5dba6c4520da7d06668f1c9f6d301e..2df2fcb1235712db38c509053e70c5cba17ef89c 100644 (file)
--- a/man/man1/g_order.1
+++ b/man/man1/g_order.1
@@ -1,7 +1,7 @@
-.TH g_order 1 "Wed 27 Feb 2002"
+.TH g_order 1 "Thu 28 Feb 2002"
 .SH NAME
 g_order
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_order\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_potential.1 b/man/man1/g_potential.1
index 40c9a52542aebac3af71d6fd43e4ed79a6181a16..9f06f0db5a00f09365a7f5a537c70a8dee0daa98 100644 (file)
--- a/man/man1/g_potential.1
+++ b/man/man1/g_potential.1
@@ -1,7 +1,7 @@
-.TH g_potential 1 "Wed 27 Feb 2002"
+.TH g_potential 1 "Thu 28 Feb 2002"
 .SH NAME
 g_potential
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_potential\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rama.1 b/man/man1/g_rama.1
index fc5888cbae5f45322f1f7b0e34f0dfaf07a02644..463448dbbdd3611c74e6d760ae497fe568e3e7eb 100644 (file)
--- a/man/man1/g_rama.1
+++ b/man/man1/g_rama.1
@@ -1,7 +1,7 @@
-.TH g_rama 1 "Wed 27 Feb 2002"
+.TH g_rama 1 "Thu 28 Feb 2002"
 .SH NAME
 g_rama
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_rama\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rdf.1 b/man/man1/g_rdf.1
index af901cef0489c29f0bec03de5edc72d1ada9c3f9..a1c8f172b7da0190328d6c787101d919d168b6ea 100644 (file)
--- a/man/man1/g_rdf.1
+++ b/man/man1/g_rdf.1
@@ -1,7 +1,7 @@
-.TH g_rdf 1 "Wed 27 Feb 2002"
+.TH g_rdf 1 "Thu 28 Feb 2002"
 .SH NAME
 g_rdf
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_rdf\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rms.1 b/man/man1/g_rms.1
index 6de7ebac815e686d74bfe2f0cd426cc80c07cbd8..0da5f7972a3649ee606ac38ff119f3ea690bd7c3 100644 (file)
--- a/man/man1/g_rms.1
+++ b/man/man1/g_rms.1
@@ -1,7 +1,7 @@
-.TH g_rms 1 "Wed 27 Feb 2002"
+.TH g_rms 1 "Thu 28 Feb 2002"
 .SH NAME
 g_rms
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_rms\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/g_rmsdist.1 b/man/man1/g_rmsdist.1
index e61950204d2f5d18d63cb49de21405d513b3fc92..8b772b2043d0ab75f0b206fb4c0d0b22898793f2 100644 (file)
--- a/man/man1/g_rmsdist.1
+++ b/man/man1/g_rmsdist.1
@@ -1,7 +1,7 @@
-.TH g_rmsdist 1 "Wed 27 Feb 2002"
+.TH g_rmsdist 1 "Thu 28 Feb 2002"
 .SH NAME
 g_rmsdist
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_rmsdist\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rmsf.1 b/man/man1/g_rmsf.1
index 52276910b7b5c5634fab9802387ffe715d4e3122..462623d01732eb372d45dd0c299a3149f76198eb 100644 (file)
--- a/man/man1/g_rmsf.1
+++ b/man/man1/g_rmsf.1
@@ -1,7 +1,7 @@
-.TH g_rmsf 1 "Wed 27 Feb 2002"
+.TH g_rmsf 1 "Thu 28 Feb 2002"
 .SH NAME
 g_rmsf
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_rmsf\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rotacf.1 b/man/man1/g_rotacf.1
index 50cfdfedcd8fb96a5a15f71b0d5a30d4748246d2..db38a84759de061f2bbe8b25adc5e0c2826ef637 100644 (file)
--- a/man/man1/g_rotacf.1
+++ b/man/man1/g_rotacf.1
@@ -1,7 +1,7 @@
-.TH g_rotacf 1 "Wed 27 Feb 2002"
+.TH g_rotacf 1 "Thu 28 Feb 2002"
 .SH NAME
 g_rotacf
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_rotacf\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_saltbr.1 b/man/man1/g_saltbr.1
index 5e3898128e96bad18a0d7d0f22f800865846b6cb..272e43e2190547629802a5b2bb397f3e60b4d4ac 100644 (file)
--- a/man/man1/g_saltbr.1
+++ b/man/man1/g_saltbr.1
@@ -1,7 +1,7 @@
-.TH g_saltbr 1 "Wed 27 Feb 2002"
+.TH g_saltbr 1 "Thu 28 Feb 2002"
 .SH NAME
 g_saltbr
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_saltbr\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_sas.1 b/man/man1/g_sas.1
index bbd7612ca5feb4ec5530ce2dd3bf9c0b6dd66f59..32af98f11bcc5c182b29655b30227eee16d993d4 100644 (file)
--- a/man/man1/g_sas.1
+++ b/man/man1/g_sas.1
@@ -1,7 +1,7 @@
-.TH g_sas 1 "Wed 27 Feb 2002"
+.TH g_sas 1 "Thu 28 Feb 2002"
 .SH NAME
 g_sas
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_sas\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_sgangle.1 b/man/man1/g_sgangle.1
index 42a84f9b8467ed4bfd1b60a72d1464b2e66d894a..afaef5f1c69b222a73ad6e1a2704c817b54bfca7 100644 (file)
--- a/man/man1/g_sgangle.1
+++ b/man/man1/g_sgangle.1
@@ -1,7 +1,7 @@
-.TH g_sgangle 1 "Wed 27 Feb 2002"
+.TH g_sgangle 1 "Thu 28 Feb 2002"
 .SH NAME
 g_sgangle
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_sgangle\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_sorient.1 b/man/man1/g_sorient.1
index 1f8741c8f4e11ae2f9cc8435f0f27f80553bc921..a4b404502d771ee689aec935f888743e56fa3ebd 100644 (file)
--- a/man/man1/g_sorient.1
+++ b/man/man1/g_sorient.1
@@ -1,7 +1,7 @@
-.TH g_sorient 1 "Wed 27 Feb 2002"
+.TH g_sorient 1 "Thu 28 Feb 2002"
 .SH NAME
 g_sorient
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_sorient\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_tcaf.1 b/man/man1/g_tcaf.1
index 4deed033db673c0ccfcda0ec0df433341d244d99..115e1d3896f31495675d1072cc9f330a6a0961be 100644 (file)
--- a/man/man1/g_tcaf.1
+++ b/man/man1/g_tcaf.1
@@ -1,7 +1,7 @@
-.TH g_tcaf 1 "Wed 27 Feb 2002"
+.TH g_tcaf 1 "Thu 28 Feb 2002"
 .SH NAME
 g_tcaf
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_tcaf\fP
 .BI "-f" " traj.trr "

diff --git a/man/man1/g_traj.1 b/man/man1/g_traj.1
index a16537651b9678fc0fed1da179d48f614ff42a40..37a46593ee57c60e0e19705beef1f971b431d0da 100644 (file)
--- a/man/man1/g_traj.1
+++ b/man/man1/g_traj.1
@@ -1,7 +1,7 @@
-.TH g_traj 1 "Wed 27 Feb 2002"
+.TH g_traj 1 "Thu 28 Feb 2002"
 .SH NAME
 g_traj
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_traj\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_velacc.1 b/man/man1/g_velacc.1
index 38fde119e0b0765fea0f04e6cb2422e3e345c65f..3688c5ba3774d95e3de8053d016d86df868ff429 100644 (file)
--- a/man/man1/g_velacc.1
+++ b/man/man1/g_velacc.1
@@ -1,7 +1,7 @@
-.TH g_velacc 1 "Wed 27 Feb 2002"
+.TH g_velacc 1 "Thu 28 Feb 2002"
 .SH NAME
 g_velacc
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3g_velacc\fP
 .BI "-f" " traj.trr "

diff --git a/man/man1/genbox.1 b/man/man1/genbox.1
index c08a67bdcfdd944bdc65905fcc2addbdb5393c7d..7f882a0d3cbf9c734045d3e53c8d8c02cbf78a8a 100644 (file)
--- a/man/man1/genbox.1
+++ b/man/man1/genbox.1
@@ -1,7 +1,7 @@
-.TH genbox 1 "Wed 27 Feb 2002"
+.TH genbox 1 "Thu 28 Feb 2002"
 .SH NAME
 genbox
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3genbox\fP
 .BI "-cp" " protein.gro "

diff --git a/man/man1/genconf.1 b/man/man1/genconf.1
index b2c92fe10deb0ffd5f57c1ac8608ecf68d2f1163..e1c882196e063324f5b7203d2eae218339115c34 100644 (file)
--- a/man/man1/genconf.1
+++ b/man/man1/genconf.1
@@ -1,7 +1,7 @@
-.TH genconf 1 "Wed 27 Feb 2002"
+.TH genconf 1 "Thu 28 Feb 2002"
 .SH NAME
 genconf
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3genconf\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/genion.1 b/man/man1/genion.1
index ec7a537e62343378c400bdb99793540909df9add..d618454dab1abf83ad9059927fd5c08d08e5f2e3 100644 (file)
--- a/man/man1/genion.1
+++ b/man/man1/genion.1
@@ -1,7 +1,7 @@
-.TH genion 1 "Wed 27 Feb 2002"
+.TH genion 1 "Thu 28 Feb 2002"
 .SH NAME
 genion
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3genion\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/genpr.1 b/man/man1/genpr.1
index 1412f1af318f7d733ccbc38e33ed90f3bbf1724a..b7f3327a84819b2c501b5e51bba9fdd7319c6930 100644 (file)
--- a/man/man1/genpr.1
+++ b/man/man1/genpr.1
@@ -1,7 +1,7 @@
-.TH genpr 1 "Wed 27 Feb 2002"
+.TH genpr 1 "Thu 28 Feb 2002"
 .SH NAME
 genpr
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3genpr\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/gmxcheck.1 b/man/man1/gmxcheck.1
index 7218e0fe66bfe28913d8fc703339c73fbe966540..53abea28ba4366c36137c3910e243a42b7cc419d 100644 (file)
--- a/man/man1/gmxcheck.1
+++ b/man/man1/gmxcheck.1
@@ -1,7 +1,7 @@
-.TH gmxcheck 1 "Wed 27 Feb 2002"
+.TH gmxcheck 1 "Thu 28 Feb 2002"
 .SH NAME
 gmxcheck
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3gmxcheck\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/gmxdump.1 b/man/man1/gmxdump.1
index d6fc34cf06662e8651cec9712dcd4ccafabf042f..bb9f720c6e414dfa4487917c2d3047a55386697c 100644 (file)
--- a/man/man1/gmxdump.1
+++ b/man/man1/gmxdump.1
@@ -1,7 +1,7 @@
-.TH gmxdump 1 "Wed 27 Feb 2002"
+.TH gmxdump 1 "Thu 28 Feb 2002"
 .SH NAME
 gmxdump
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3gmxdump\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/grompp.1 b/man/man1/grompp.1
index d46cc763eab6effbaf51fc642430d76eb909b8c1..e4a45d787c42e38162800ca85a30bf3076a84d2a 100644 (file)
--- a/man/man1/grompp.1
+++ b/man/man1/grompp.1
@@ -1,7 +1,7 @@
-.TH grompp 1 "Wed 27 Feb 2002"
+.TH grompp 1 "Thu 28 Feb 2002"
 .SH NAME
 grompp
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3grompp\fP
 .BI "-f" " grompp.mdp "

diff --git a/man/man1/highway.1 b/man/man1/highway.1
index bd966b743153049e7d49277dd5a3fd5a20beae5a..a005fa0c3fce6251f2516e6a2f885b78ffe3d319 100644 (file)
--- a/man/man1/highway.1
+++ b/man/man1/highway.1
@@ -1,7 +1,7 @@
-.TH highway 1 "Wed 27 Feb 2002"
+.TH highway 1 "Thu 28 Feb 2002"
 .SH NAME
 highway
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3highway\fP
 .BI "-f" " highway.dat "

diff --git a/man/man1/make_ndx.1 b/man/man1/make_ndx.1
index 06828c38f86504333fa09a30480b1492c5b32903..09fc349b10861ad60f7614fa98e099532e494be4 100644 (file)
--- a/man/man1/make_ndx.1
+++ b/man/man1/make_ndx.1
@@ -1,7 +1,7 @@
-.TH make_ndx 1 "Wed 27 Feb 2002"
+.TH make_ndx 1 "Thu 28 Feb 2002"
 .SH NAME
 make_ndx
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3make_ndx\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/mdrun.1 b/man/man1/mdrun.1
index 14fd9888358c0fe51e3cfee1f5626d7c6d3f03ba..3707edf79641b54d6844df062ebd0df0c8fdc8c0 100644 (file)
--- a/man/man1/mdrun.1
+++ b/man/man1/mdrun.1
@@ -1,7 +1,7 @@
-.TH mdrun 1 "Wed 27 Feb 2002"
+.TH mdrun 1 "Thu 28 Feb 2002"
 .SH NAME
 mdrun
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3mdrun\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/mk_angndx.1 b/man/man1/mk_angndx.1
index 486194979d1dcccbd099730a3a5aed8e773ed797..b277cd75e7fda73a8632a7c64ba3b8b6dc0881df 100644 (file)
--- a/man/man1/mk_angndx.1
+++ b/man/man1/mk_angndx.1
@@ -1,7 +1,7 @@
-.TH mk_angndx 1 "Wed 27 Feb 2002"
+.TH mk_angndx 1 "Thu 28 Feb 2002"
 .SH NAME
 mk_angndx
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3mk_angndx\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/ngmx.1 b/man/man1/ngmx.1
index 162d3dc815e559be1d4efed17afd01932231aabf..6cec43caf97adea1aa333e7939371c882af14ba8 100644 (file)
--- a/man/man1/ngmx.1
+++ b/man/man1/ngmx.1
@@ -1,7 +1,7 @@
-.TH ngmx 1 "Wed 27 Feb 2002"
+.TH ngmx 1 "Thu 28 Feb 2002"
 .SH NAME
 ngmx
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3ngmx\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/pdb2gmx.1 b/man/man1/pdb2gmx.1
index a35718ebd9f6a2b0d655a472795c026d2bad4f47..f39822f897dfbd9a648920bcd4f3a700d957e7a8 100644 (file)
--- a/man/man1/pdb2gmx.1
+++ b/man/man1/pdb2gmx.1
@@ -1,7 +1,7 @@
-.TH pdb2gmx 1 "Wed 27 Feb 2002"
+.TH pdb2gmx 1 "Thu 28 Feb 2002"
 .SH NAME
 pdb2gmx
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3pdb2gmx\fP
 .BI "-f" " eiwit.pdb "

diff --git a/man/man1/protonate.1 b/man/man1/protonate.1
index 86de7ded2cd952791a54f06ca686448734119699..a000f946d94cd7b57358971f6652026f801ca337 100644 (file)
--- a/man/man1/protonate.1
+++ b/man/man1/protonate.1
@@ -1,7 +1,7 @@
-.TH protonate 1 "Wed 27 Feb 2002"
+.TH protonate 1 "Thu 28 Feb 2002"
 .SH NAME
 protonate
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3protonate\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/tpbconv.1 b/man/man1/tpbconv.1
index 115e15629bb8030a0dc188f65361ea74b3be3e13..05e19dee9b5bb1f24db31b0a1ce8fe490056ef9d 100644 (file)
--- a/man/man1/tpbconv.1
+++ b/man/man1/tpbconv.1
@@ -1,7 +1,7 @@
-.TH tpbconv 1 "Wed 27 Feb 2002"
+.TH tpbconv 1 "Thu 28 Feb 2002"
 .SH NAME
 tpbconv
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3tpbconv\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/trjcat.1 b/man/man1/trjcat.1
index 5e903df5b5d0f0575b78303b865cc08da1ad886d..98806c36d9583d1804b5c15ab89df99f12f8fd9d 100644 (file)
--- a/man/man1/trjcat.1
+++ b/man/man1/trjcat.1
@@ -1,7 +1,7 @@
-.TH trjcat 1 "Wed 27 Feb 2002"
+.TH trjcat 1 "Thu 28 Feb 2002"
 .SH NAME
 trjcat
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3trjcat\fP
 .BI "-o" " trajout.xtc "

diff --git a/man/man1/trjconv.1 b/man/man1/trjconv.1
index ceb6d573b10468178b3cb0c832bbb1be03eb05ce..0b35b4f6589b73e6ab977beb6c5cb7560321748b 100644 (file)
--- a/man/man1/trjconv.1
+++ b/man/man1/trjconv.1
@@ -1,7 +1,7 @@
-.TH trjconv 1 "Wed 27 Feb 2002"
+.TH trjconv 1 "Thu 28 Feb 2002"
 .SH NAME
 trjconv
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3trjconv\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/trjorder.1 b/man/man1/trjorder.1
index e8ff3c9be02cef6be463669bda85cab68f73b68e..1d90f094598e2a74c166aa57a99e54d338846a18 100644 (file)
--- a/man/man1/trjorder.1
+++ b/man/man1/trjorder.1
@@ -1,7 +1,7 @@
-.TH trjorder 1 "Wed 27 Feb 2002"
+.TH trjorder 1 "Thu 28 Feb 2002"
 .SH NAME
 trjorder
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3trjorder\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/wheel.1 b/man/man1/wheel.1
index ad6398561c0a6a42c6f3090919e3f5348b01fcfd..5ac4a9db7bfa368db987beca85f31c08a4d09d48 100644 (file)
--- a/man/man1/wheel.1
+++ b/man/man1/wheel.1
@@ -1,7 +1,7 @@
-.TH wheel 1 "Wed 27 Feb 2002"
+.TH wheel 1 "Thu 28 Feb 2002"
 .SH NAME
 wheel
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3wheel\fP
 .BI "-f" " nnnice.dat "

diff --git a/man/man1/x2top.1 b/man/man1/x2top.1
index 2dedb81e83ec91449af9949c733585fae5f1db32..410d0c65ff02459da2254e6e121d544d68ac438a 100644 (file)
--- a/man/man1/x2top.1
+++ b/man/man1/x2top.1
@@ -1,7 +1,7 @@
-.TH x2top 1 "Wed 27 Feb 2002"
+.TH x2top 1 "Thu 28 Feb 2002"
 .SH NAME
 x2top
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3x2top\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/xpm2ps.1 b/man/man1/xpm2ps.1
index ecfcc7a7773056741b7dadd1e3156a7432f276a3..50e47baae276a38f33be49de1b5f294b6c83b5fc 100644 (file)
--- a/man/man1/xpm2ps.1
+++ b/man/man1/xpm2ps.1
@@ -1,7 +1,7 @@
-.TH xpm2ps 1 "Wed 27 Feb 2002"
+.TH xpm2ps 1 "Thu 28 Feb 2002"
 .SH NAME
 xpm2ps
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3xpm2ps\fP
 .BI "-f" " root.xpm "

diff --git a/man/man1/xrama.1 b/man/man1/xrama.1
index 396217173adb61219fd4206d87107d114e4b5859..32e6b93e70dc070d3e10e30dff9de2211c722dab 100644 (file)
--- a/man/man1/xrama.1
+++ b/man/man1/xrama.1
@@ -1,7 +1,7 @@
-.TH xrama 1 "Wed 27 Feb 2002"
+.TH xrama 1 "Thu 28 Feb 2002"
 .SH NAME
 xrama
-.B VERSION 3.1.beta_20020215
+.B VERSION 3.1
 .SH SYNOPSIS
 \f3xrama\fP
 .BI "-f" " traj.xtc "

diff --git a/share/html/gmxfaq.html b/share/html/gmxfaq.html
index 3c4269737abb14484d4de1712763df65423c836b..e77461b1883d8ee9ea710244a6a55c4d55de04b2 100644 (file)
--- a/share/html/gmxfaq.html
+++ b/share/html/gmxfaq.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>FAQ</h2><font size=-1><A HREF="online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Mon 23 Jul 2001</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
  
 <p>If you don't find the solution to your problem here, you could have a look in 
@@ -23,6 +23,7 @@ Developer info that you could use, and when all else fails it's
 time to post your question to the mailing lists!</p>
 
 
+
 <h3>Download & Installation</h3>
 
 <ul>
@@ -37,8 +38,12 @@ do I install it?</A>
 still says it can't find it!</A>
 <li><A HREF="#MPI">How do I compile GROMACS for parallel runs?</A>
 <li><A HREF="#noMPIwrapper">When I enable MPI support for parallel runs, GROMACS
-looks for a special MPI compiler, but we don't use that; can't I add the MPI library
-manually with -lmpi ?</A>
+looks for a special MPI wrapper script like 'mpicc', but we don't use that; is it possible to
+ add the MPI library manually with -lmpi ?</A>
+<li><A HREF="#nomotif">How do I turn off Motif?</A>
+<li><A HREF="#ldpath">Everything compiles fine, but when I try to run a program
+it complains about not finding libXXXX.so.</A>
+<li><A HREF="#osx_zsh">I get an error from the configure script on Mac OS X!</A>
 <li><A HREF="#noclue">It still won't compile and I haven't got a clue what the problem might be...</A>
 <li><A HREF="#relativespeed">How fast is GROMACS compared to other programs?</A>
 <li><A HREF="#speed">Is there any way I can make GROMACS run faster?</A>
@@ -57,6 +62,7 @@ to simulate. What should I do?</A>
 file to a .pdb file?</A> 
 <li><A HREF="#scmis">The <TT>pdb2gmx</TT> program is complaining about long bonds and/or
 missing atoms. What should I do?</A>
+<li><A HREF="#osxcpp">grompp doesn't find the C preprocessor /lib/cpp on OS X!</A>
 </ul><br>
 
 <h3>Simulation</h3>
@@ -68,6 +74,8 @@ missing atoms. What should I do?</A>
 <li><A HREF="#temp">Why do I get very strange temperatures in my simulation?</A>
 <li><A HREF="#simann">Why do I get very strange temperatures in simulated annealing?</A>
 <li><A HREF="#recover">Is there any smart way to continue a run that crashed?</A>
+<li><A HREF="#largefiles">When my trajectory files reach 2GB I get strange error messages,
+or they just disappear. Why?</A>
 </ul><br>
 
 <h3>Analysis</h3>
@@ -133,7 +141,7 @@ If you're impatient you could just unpack the distribution and try<br><br>
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt>
  ./configure<br>
  make<br>
@@ -144,16 +152,16 @@ If you're impatient you could just unpack the distribution and try<br><br>
 <br>
 
 The configure script will complain if it doesn't find FFTW, but you will be told what to do.<br><br>
-This setup is new for version 3.0, so there might be some bugs we've missed, though. Don't
-hesitate to post questions to the mailing lists or contact us at 
-<A HREF="mailto:gromacs@gromacs.org">gromacs@gromacs.org</A> if you have problems.<br><br>
+This setup is new from version 3.0, so there might be some bugs we've missed, though. Don't
+hesitate to post questions to the <a href="http://www.gromacs.org/mailing_lists/users.php>mailing lists</a> 
+if you have problems.<br><br>
 
 <li><A NAME="compiler">
 <B>How do I select the compiler and/or flags to use?</B><br><br>
 Select the compiler by setting the CC and/or F77 environment variables before running the
 GROMACS configure script (MPICC for the MPI C compiler). You can also set the corresponding compiler flags with CFLAGS and
 FFLAGS, and the linker flags with LDFLAGS. If you want to add a library at the link stage
-you can add the -llib flags to the LDADD variable, and include directories can be 
+you can add the -llib flags to the LIBS variable, and include directories can be 
 added in the CPPFLAGS variable.<br><br>
 
 <li><A NAME="fftw">
@@ -169,7 +177,7 @@ Configure and install FFTW with the command:<br><br>
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt> ./configure --enable-float<br>
  make<br>
  make install</TT>
@@ -185,7 +193,7 @@ of FFTW (nice to have) with:<br><br>
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt> make distclean<br>
  ./configure<br>
  make<br>
@@ -209,7 +217,7 @@ Specify the header file directory (e.g. /home/erik/fftw/include) as<br><br>
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt> CPPFLAGS="-I/home/erik/fftw/include"</tt>
 <td></td>
 </tr>
@@ -220,7 +228,7 @@ and the location of the libraries (e.g. /home/erik/fftw/lib) in<br><br>
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt> LDFLAGS="-L/home/erik/fftw/lib"</tt>
 <td></td>
 </tr>
@@ -251,13 +259,75 @@ is set. Check the options to the configure script with "./configure --help".
 
 <li><A NAME="noMPIwrapper">
 <B>When I enable MPI support for parallel runs, GROMACS
-looks for a special MPI compiler, but we don't use that; can't I add the MPI library
-manually with -lmpi ?</B><br><br>
-Yes, you can, but don't add it to the compiler name! If you have to provide a flag
-to search the MPI include directory you should add it in the CPPFLAGS variable, and the
-library directory might have to be added in the LDFLAGS variable (check the FFTW section
-for details.) The actual MPI library flag "-lmpi" should be added in the LDADD environment 
-variable, so GROMACS adds this library when linking.<br><br>
+looks for a special MPI wrapper script like 'mpicc', but we don't use that; is it possible to
+ add the MPI library manually with -lmpi ?</B><br><br>
+Sure - no problem, but it might not be entirely obvious if you are new to autoconf scripts.
+Here's how to do it:<br><br>
+To use the MPI library we need the header files (mpi.h) with definitions, and the MPI libraries
+with the actual code (e.g. libmpi.a). If your system uses some special hardware it might
+also be necessary to link with more libraries - ask your system administrator if you have
+any problems. Start by location these headers and libraries on your system, and then add
+them to your environment variables before running the configure script:
+<br><br>
+<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
+<tr NOSAVE>
+<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
+<td WIDTH="90%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<tt>
+setenv CPPFLAGS "-I/path/to/your/mpi/include"<br>
+setenv LDFLAGS "-L/path/to/your/mpi/lib"<br>
+setenv LIBS "-lmpi"<br>
+setenv MPICC "cc"</tt>
+<td></td>
+</tr>
+</table>
+<br>
+(This is valid for tcsh, for bash you should use export instead.) Note that these commands overwrite 
+any previous assignments, so you must add
+all parts you want (you can use $VARIABLE to add the previous value of an environment variable).
+<br>
+Now you should be able to run ./configure --enable-mpi !
+<br><br>
+
+<li><A NAME="nomotif">
+<B>How do I turn off Motif?</b><br><br>
+Just use the flag --without-motif-libraries (or headers).
+If the configure script doesn't find both libraries and headers it will disable motif. This is useful when you have motif on the machine where you compile, but not on all machines you run on.<br><br>
+
+<li><A NAME="ldpath">
+<b>Everything compiles fine, but when I try to run a program
+it complains about not finding libXXXX.so.</b><br><br>
+GROMACS and/or the FFTW package can be compiled with shared libraries. In fact,
+it's the default setup in the Linux RPMs. This means we save space by not linking all the
+routines into each binary, but call the shared library at runtime. Of course, this requires that you can find the library at runtime. For the GROMACS distribution programs we hardcode the location of the GROMACS and FFTW libraries, but if you compile your own programs or move your libraries you must tell the system where to find them! 
+Fortunately, this is quite easy to do. On Linux you can do it permanently for
+all users if you are root, by adding the search path to the file /etc/ld.so.conf. Alternatively, you can add it to the LD_LIBRARY_PATH environment variable:
+<br><br>
+<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
+<tr NOSAVE>
+<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
+
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<TT>setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH:/opt/lib"</TT>
+<td></td>
+</tr>
+</table>
+<br>
+(This is valid for tcsh, for bash you should use export instead.) Ask your
+local sysadm how to add it to your login file so it's done automatically each
+time you log on.
+<br><br>
+
+
+<li><A NAME="osx_zsh">
+<b>I get an error from the configure script on Mac OS X!</B><br><br>
+This is because OS X uses Z shell for /bin/sh. This will hopefully be
+fixed in a future release of automake (it is not caused by Gromacs), but in the
+meantime you can install bash (if you don't already have it) and 
+use the command '/bin/bash ./configure'  (Your bash location might be different from /bin/bash).
+<br><br>
+
+
 
 <li><A NAME="noclue">
 <B>It still won't compile and I haven't got a clue what the problem might be...</B><br><br>
@@ -301,7 +371,7 @@ you should use the Compaq compilers instead of gcc.<br><br>
 You should always use single precision; there are very few cases where you
 actually need double precision, and it's slower.<br><br>
 Investigate the options <TT>-dummy</TT> and <TT>-heavyh</TT> to
-<A HREF="documentation/reference3.0/online/pdb2gmx.html"><TT>pdb2gmx</TT></A> 
+<A HREF="/documentation/reference_3.1/online/pdb2gmx.html"><TT>pdb2gmx</TT></A> 
 which control the constraining of hydrogen atoms and the mass of
 unconstrained hydrogen atoms. This eliminates the highest freqency
 motions in your system, enabling you to increase the timestep without
@@ -350,10 +420,10 @@ still prints fine on paper.<br><br>
 <li><A NAME="PDB">
 <B>OK, I've downloaded a PDB file with a structure I'd like
 to simulate. What should I do?</B><br><br>
-Look at the <A HREF="/documentation/reference3.0/online/flow.html">flowchart</A> for a quick overview. 
+Look at the <A HREF="/documentation/reference_3.1/online/flow.html">flowchart</A> for a quick overview. 
 Start where it says "eiwit.pdb" (this is somewhere at the top). 
 More detailed info can be found in the 
-<A HREF="/documentation/reference3.0/online/getting_started.html">Getting Started</A>
+<A HREF="/documentation/reference_3.1/online/getting_started.html">Getting Started</A>
 section, you can probably start where it says "Ribonuclease S-Peptide".
 <br><br>
 
@@ -367,16 +437,16 @@ have different chain identifiers!<br><br>
 <li><A NAME="convert">
 <B>How do I convert my structure from a .gro, .tpr, or trajectory 
 file to a .pdb file?</B><br><br>
-Any <a href="/documentation/reference3.0/online/files.html">generic structure</a> file,
+Any <a href="/documentation/reference_3.1/online/files.html">generic structure</a> file,
 for instance <TT>.gro</TT>, <TT>.pdb</TT> or <TT>.tpr</TT>, can be
 converted to <TT>.pdb</TT> with 
-<a href="/documentation/reference3.0/online/editconf.html">editconf</a></TT>.  You can view a
+<a href="/documentation/reference_3.1/online/editconf.html">editconf</a></TT>.  You can view a
 <TT>.pdb</TT> file with several programs, for instance <TT>rasmol</TT>. Two generic
 structure files can be fitted with 
-<a href="/documentation/reference3.0/online/g_confrms.html">g_confrms</a></TT>, the two
+<a href="/documentation/reference_3.1/online/g_confrms.html">g_confrms</a></TT>, the two
 superimposed structures can be written to a <TT>.pdb</TT> file.  Any
-<a href="/documentation/reference3.0/online/files.html">generic trajectory</a> format can be
-converted with <a href="/documentation/reference3.0/online/trjconv.html"><TT>trjconv</TT></a>.
+<a href="/documentation/reference_3.1/online/files.html">generic trajectory</a> format can be
+converted with <a href="/documentation/reference_3.1/online/trjconv.html"><TT>trjconv</TT></a>.
 You can dump one frame with <TT>trjconv -dump</TT>, or write a
 <TT>.pdb</TT> with multiple frames using <TT>trjconv -op -app</TT>.
 If multiple structures in a <TT>.pdb</TT> are separated by
@@ -388,14 +458,22 @@ view them.<br><br>
 <B>The <TT>pdb2gmx</TT> program is complaining about long bonds and/or
 missing atoms. What should I do?</B><br><br>
 There are probably atoms missing earlier in the 
-<A HREF="/documentation/reference3.0/online/pdb.html"><TT>.pdb</TT></A> file
-which makes <A HREF="/documentation/reference3.0/online/pdb2gmx.html"><TT>pdb2gmx</TT></A>
+<A HREF="/documentation/reference_3.1/online/pdb.html"><TT>.pdb</TT></A> file
+which makes <A HREF="/documentation/reference_3.1/online/pdb2gmx.html"><TT>pdb2gmx</TT></A>
 go crazy. Check the screen output of <TT>pdb2gmx</TT>, as it
 will tell you which one is missing. Then add the atoms in your pdb file,
 energy minimization will put them in the right place, 
 or fix the side chain with e.g. the 
 <A HREF="http://swift.embl-heidelberg.de/whatif/">WhatIF program</A>.<br><br>
 
+<li><A NAME="osxcpp">
+<B>grompp doesn't find the C preprocessor /lib/cpp on OS X!</B><br><br>
+Yep, that's right. OS X is a real Unix system, but Apple have been moving
+some stuff around. Look for it in /usr/bin or possible a place like
+/usr/libexec/gcc/darwin/ppc/2.95.2/cpp. Since a lot of programs assume
+cpp to be present in /lib it is probably smart to make a link, but you
+can also specify the location with the cpp keyword in your mdp files.
+<br><br>
 
 <li><A NAME="1-4cut">
 <B>What does "1-4 (#,#) interaction not within cut-off" mean?</B><br><br>
@@ -446,20 +524,23 @@ usually result in a large percentage of CPU time being devoted to
 machine with <TT>top</TT> and <TT>osview</TT>).
 
 <LI>You might have all 
-<A HREF="/documentation/reference3.0/online/mdp_opt.html#out"><TT>nst*</TT></A> parameters (see
-your <A HREF="/documentation/reference3.0/online/mdp_opt.html"><TT>.mdp</TT></A> file) set to 0,
+<A HREF="/documentation/reference_3.1/online/mdp_opt.html#out"><TT>nst*</TT></A> parameters (see
+your <A HREF="/documentation/reference_3.1/online/mdp_opt.html"><TT>.mdp</TT></A> file) set to 0,
 this will suppress most output.
 
 <LI>Your disk might be full. Eventually this will lead to
 <TT>mdrun</TT> crashing, but since output is buffered, it might take a
 while for <TT>mdrun</TT> to realize it can't write.
+<li>You are runnning an executable compiled with MPI support (e.g. 
+<a href="http://www.lam-mpi.org">LAM</a>) and did not start the LAM daemon
+(lamboot). See LAM documentation.
 </UL>
 <br><br>
 
 <li><A NAME="temp">
 <b>Why do I get very strange temperatures in my simulation?</b><br><br>
 If you are using simulated annealing 
-(see <A HREF=/documentation/reference3.0/online/mdp_opt.html#sa><TT>.mdp</TT> options</A>), 
+(see <A HREF=/documentation/reference_3.1/online/mdp_opt.html#sa><TT>.mdp</TT> options</A>), 
 check out <A HREF="#simann">the next item</A>. 
 If you are not using simulated annealing, you might have very close contacts or a too large time
 step. This causes inaccurate integration which will usually result in
@@ -472,8 +553,8 @@ short equilibration run with a small(er) time step.  <br><br>
 This probably means that the initial time in your simulation is
 not zero ps. The temperature during simulated annealing is controlled
 by two points on a linear curve: temperature will be zero K at
-<A HREF=/documentation/reference3.0/online/mdp_opt.html#sa><TT>zero_temp_time</TT></A> ps and it
-will be <A HREF=/documentation/reference3.0/online/mdp_opt.html#sa><TT>ref_t</TT></A> K at zero
+<A HREF=/documentation/reference_3.1/online/mdp_opt.html#sa><TT>zero_temp_time</TT></A> ps and it
+will be <A HREF=/documentation/reference_3.1/online/mdp_opt.html#sa><TT>ref_t</TT></A> K at zero
 ps. This means that if you do not start your simulation at zero ps,
 the simulation will not start at <TT>ref_t</TT> K. So if your
 <TT>zero_temp_time</TT> is positive and the starting time for your
@@ -504,23 +585,23 @@ graphs are included to clarify things a bit.<br><br>
 Yes, if the reason for the crash didn't have anything to doe with
 the algorithms, i.e. it was due to a system crash, a full disk, or
  a kill by the queuing system.  Otherwise you'll have to use 
-<TT><a href="/documentation/reference3.0/online/grompp.html">grompp</a></TT>
+<TT><a href="/documentation/reference_3.1/online/grompp.html">grompp</a></TT>
 and change the options.
 
 To really continue a simulation as if nothing had happened, you will
 need coordinates and velocities in full precision (i.e. 
-<TT><a href="/documentation/reference3.0/online/trr.html">.trr</a></TT> format). 
-<TT><a href="/documentation/reference3.0/online/xtc.html">.xtc</a></TT> trajectories are in
+<TT><a href="/documentation/reference_3.1/online/trr.html">.trr</a></TT> format). 
+<TT><a href="/documentation/reference_3.1/online/xtc.html">.xtc</a></TT> trajectories are in
 reduced precision (only 3 decimal places after the decimal point) and
 do not contain velocity information at all. Feed this trajectory and
-your origional <TT><a href="/documentation/reference3.0/online/tpr.html">.tpr</a></TT> file to
-<TT><a href="/documentation/reference3.0/online/tpbconv.html">tpbconv</a></TT> to obtain a new
-<TT><a href="/documentation/reference3.0/online/tpr.html">.tpr</a></TT> file, <EM>be sure</EM>
+your origional <TT><a href="/documentation/reference_3.1/online/tpr.html">.tpr</a></TT> file to
+<TT><a href="/documentation/reference_3.1/online/tpbconv.html">tpbconv</a></TT> to obtain a new
+<TT><a href="/documentation/reference_3.1/online/tpr.html">.tpr</a></TT> file, <EM>be sure</EM>
 to specify the one-but-last frame from your 
-<TT><a href="/documentation/reference3.0/online/trr.html">.trr</a></TT> file, since the very
+<TT><a href="/documentation/reference_3.1/online/trr.html">.trr</a></TT> file, since the very
 last frame is likely to be corrupted due to the crash. With the 
-<TT><a href="/documentation/reference3.0/online/tpr.html">.tpr</a></TT> file 
-<TT><a href="/documentation/reference3.0/online/tpbconv.html">tpbconv</a></TT> produces you can
+<TT><a href="/documentation/reference_3.1/online/tpr.html">.tpr</a></TT> file 
+<TT><a href="/documentation/reference_3.1/online/tpbconv.html">tpbconv</a></TT> produces you can
 restart your simulation.<br><br>
 
 After the continuation run is finished, you will have your simulation
@@ -530,7 +611,7 @@ This can be done as follows (the same command works for xtc-files):<br><br>
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <TT>trjcat -o whole.trr part1.trr part2.trr part3.trr</TT>
 <td></td>
 </tr>
@@ -540,7 +621,7 @@ The energy files can be concatenated in a similar manner:<br><br>
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <TT>eneconv -o whole.edr part1.edr part2.edr part3.edr</TT>
 <td></td>
 </tr>
@@ -553,30 +634,46 @@ runs continued with tpbconv and grompp you might have to set the times yourself
 <br><br>
 
 It is of course possible to start a simulation from the coordinates in
-your <a href="/documentation/reference3.0/online/xtc.html">xtc</a> file, but in that case new
+your <a href="/documentation/reference_3.1/online/xtc.html">xtc</a> file, but in that case new
 velocities will have to be generated resulting in a 'kink' in the
 simulation. To prevent this you should write coordinates and
-velocities to a <TT><a href="/documentation/reference3.0/online/trr.html">.trr</a></TT> file
+velocities to a <TT><a href="/documentation/reference_3.1/online/trr.html">.trr</a></TT> file
 during your simulations.  Do this by setting 
-<A HREF=/documentation/reference3.0/online/mdp_opt.html#out><TT>nstxout</TT></a> and 
-<A HREF=/documentation/reference3.0/online/mdp_opt.html#out><TT>nstvout</TT></a> in your 
-<TT><a href="/documentation/reference3.0/online/mdp.html">.mdp</a></TT> file. You don't need
+<A HREF=/documentation/reference_3.1/online/mdp_opt.html#out><TT>nstxout</TT></a> and 
+<A HREF=/documentation/reference_3.1/online/mdp_opt.html#out><TT>nstvout</TT></a> in your 
+<TT><a href="/documentation/reference_3.1/online/mdp.html">.mdp</a></TT> file. You don't need
 these frames very often (every 10 ps or so), but remember that when
-<TT><a href="/documentation/reference3.0/online/mdrun.html">mdrun</a></TT> crashes, everything
+<TT><a href="/documentation/reference_3.1/online/mdrun.html">mdrun</a></TT> crashes, everything
 calculated after the last frame in the <TT><a
-href="/documentation/reference3.0/online/trr.html">.trr</a></TT> file, will have to be
+href="/documentation/reference_3.1/online/trr.html">.trr</a></TT> file, will have to be
 recalculated for a proper continuation.<br><br>
 
+<li><A NAME="largefiles">
+<b>When my trajectory files reach 2GB I get strange error messages,
+or they just disappear. Why?</b><br><br>
+This is a problem with the file system; when the system, or the C library,
+or the compiler, or the NFS implementation (version 2) only uses 32 bits
+for the file pointer you cannot use files larger than 2GB. On most modern
+systems there are special compiler flags you can set to enable 64-bit file
+pointers, but since the autoconf test for this doesn't work we have chosen
+not to include any flags by default, since it can break other things. But
+you can of course try anything if you add your own flags :-)
+<br>
+In any case, it is probably a good idea to try to keep your files
+smaller than 2GB. You never know if you later might need to use it over
+NFS version 2 or on some supercomputer system that doesn't support large
+files yet.<br><br>
+
 
 <li><A NAME="multPDB">
 <b>How do I analyze a PDB file with multiple entries?</b><br><br>
 Assuming your 
-<A HREF="/documentation/reference3.0/online/pdb.html"><TT>.pdb</TT></A> file is
+<A HREF="/documentation/reference_3.1/online/pdb.html"><TT>.pdb</TT></A> file is
 called "<TT>eiwit.pdb</TT>", this is what you would do:<br><br>
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <TT>pdb2gmx -f eiwit.pdb -reth -ter -n</TT>
 <td></td>
 </tr>
@@ -584,18 +681,18 @@ called "<TT>eiwit.pdb</TT>", this is what you would do:<br><br>
 <br>
 
 <TT>-reth</TT> lets 
-<A HREF="/documentation/reference3.0/online/pdb2gmx.html"><TT>pdb2gmx</TT></A> keep all
+<A HREF="/documentation/reference_3.1/online/pdb2gmx.html"><TT>pdb2gmx</TT></A> keep all
 hydrogens which are present in your input file. It will also <B>not
 add</B> any missing hydrogens, so your molecules should be
 complete. <TT>-ter</TT> will cause <TT>pdb2gmx</TT> to ask for termini
 types for which you must select 'none' for both C- and N-terminus.
 <TT>-n</TT> tells <TT>pdb2gmx</TT> to generate a 
-<A HREF="/documentation/reference3.0/online/ndx.html"><TT>.ndx</TT></A> file with the atoms
+<A HREF="/documentation/reference_3.1/online/ndx.html"><TT>.ndx</TT></A> file with the atoms
 reordered to the GROMACS standard. <TT>pdb2gmx</TT> now generates a
-topology file (<A HREF="/documentation/reference3.0/online/top.html"><TT>topol.top</TT></A>)
+topology file (<A HREF="/documentation/reference_3.1/online/top.html"><TT>topol.top</TT></A>)
 which exactly corresponds with the molecule(s) in your input file.
 It also writes a coordinate file 
-(<A HREF="/documentation/reference3.0/online/gro.html"><TT>conf.gro</TT></A>).<br><br>
+(<A HREF="/documentation/reference_3.1/online/gro.html"><TT>conf.gro</TT></A>).<br><br>
 
 <P>
 The next step is:
@@ -603,7 +700,7 @@ The next step is:
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt>trjconv -f eiwit.pdb -o eiwit.xtc -n clean -timestep 1 -box 10 -center</tt>
 <td></td>
 </tr>
@@ -611,12 +708,12 @@ The next step is:
 <br>
 
 Yes, <TT>-f eiwit.pdb</TT> works because a <TT>.pdb</TT> is also a
-<A HREF="/documentation/reference3.0/online/files.html">trajectory format</A>
+<A HREF="/documentation/reference_3.1/online/files.html">trajectory format</A>
 in GROMACS. <TT>-ox</TT> sets output to 
-<A HREF="/documentation/reference3.0/online/xtc.html"><TT>.xtc</TT></A>. <TT>-n clean</TT>
-tells <A HREF="/documentation/reference3.0/online/trjconv.html"><TT>trjconv</TT></A> to
+<A HREF="/documentation/reference_3.1/online/xtc.html"><TT>.xtc</TT></A>. <TT>-n clean</TT>
+tells <A HREF="/documentation/reference_3.1/online/trjconv.html"><TT>trjconv</TT></A> to
 use the <TT>clean.ndx</TT> generated by 
-<A HREF="/documentation/reference3.0/online/pdb2gmx.html"><TT>pdb2gmx</TT></A>, so the atom
+<A HREF="/documentation/reference_3.1/online/pdb2gmx.html"><TT>pdb2gmx</TT></A>, so the atom
 ordering in the output (<TT>.xtc</TT>) file will be according to GROMACS
 standards. <TT>-timestep 1</TT> sets the timestep between output frames
 to one, so the structures from the <TT>.pdb</TT> file get numbered 
@@ -638,7 +735,7 @@ A not very exiting but mandatory step is:<br><br>
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt>
 grompp -f grompp.mdp -c conf.gro -p topol.top</tt>
 <td></td>
@@ -647,13 +744,13 @@ grompp -f grompp.mdp -c conf.gro -p topol.top</tt>
 <br>
 
 This will generate a run input file 
-(<A HREF="/documentation/reference3.0/online/tpr.html"><TT>topol.tpr</TT></A>) from the 
+(<A HREF="/documentation/reference_3.1/online/tpr.html"><TT>topol.tpr</TT></A>) from the 
 <TT>topol.top</TT> and <TT>conf.gro</TT> you generated with 
 <TT>pdb2gmx</TT>. 
-A <A HREF="/documentation/reference3.0/online/mdp.html">default <TT>grompp.mdp</TT></A> is 
+A <A HREF="/documentation/reference_3.1/online/mdp.html">default <TT>grompp.mdp</TT></A> is 
 available. You can probably use it 'as is', but you might want or need 
 to modify some thing. In any case you are encouraged to 
-<A HREF="/documentation/reference3.0/online/mdp_opt.html">review the description</A> of the 
+<A HREF="/documentation/reference_3.1/online/mdp_opt.html">review the description</A> of the 
 numerous options in the <TT>.mdp</TT> file.
 
 <P>
@@ -662,7 +759,7 @@ structures. Enter:<br><br>
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt>
 g_rms -f eiwit.xtc -s topol.tpr -m</tt>
 <td></td>
@@ -671,15 +768,15 @@ g_rms -f eiwit.xtc -s topol.tpr -m</tt>
 <br>
 
 <TT>-f eiwit.xtc</TT> and <TT>-s topol.tpr</TT> are self-explanatory.
-<TT>-m</TT> tells <A HREF="/documentation/reference3.0/online/g_rms.html"><TT>g_rms</TT></A>
+<TT>-m</TT> tells <A HREF="/documentation/reference_3.1/online/g_rms.html"><TT>g_rms</TT></A>
 to output an RMSD matrix in 
-<A HREF="/documentation/reference3.0/online/xpm.html"><TT>.xpm</TT></A> format, which can be
+<A HREF="/documentation/reference_3.1/online/xpm.html"><TT>.xpm</TT></A> format, which can be
 directly viewed with for example <TT>xv</TT>.
 
 <P>
 Of course there are many more analysis tools available. For example
-<A HREF="/documentation/reference3.0/online/ngmx.html"><TT>ngmx</TT></A> a trajectory viewer.
-A list of all tools is available in the <A HREF="/documentation/reference3.0/online.html">online
+<A HREF="/documentation/reference_3.1/online/ngmx.html"><TT>ngmx</TT></A> a trajectory viewer.
+A list of all tools is available in the <A HREF="/documentation/reference_3.1/online.html">online
 manual</A>.
 
 <P>
@@ -691,14 +788,14 @@ Yes, just type:<br><br>
 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 <tr NOSAVE>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+<td WIDTH="98%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt>g_confrms -f1 file1.xxx -f2 file2.xxx</tt>
 <td></td>
 </tr>
 </table>
 <br>
 g_confrms accepts 
-any <A HREF="/documentation/reference3.0/online/files.html">generic structure format</A> which 
+any <A HREF="/documentation/reference_3.1/online/files.html">generic structure format</A> which 
 for instance can be <TT>.pdb</TT>, <TT>.gro</TT> or <TT>.tpr</TT>.
 The program will ask you to select subgroups of both structures for the
 (non mass weighted) LSQ fit. These subgroups must have the same number of atoms, however the two 
@@ -715,8 +812,8 @@ on top of each other.
 <li><A NAME="group">
 <b>I get tired of having to select the same index group 
 over and over again. Is there a better way to do it?</b><br><br>
-Use <A HREF="/documentation/reference3.0/online/make_ndx.html"><TT>make_ndx</TT></A> to create 
-an <A HREF="/documentation/reference3.0/online/ndx.html"><TT>.ndx</TT></A> file with only one
+Use <A HREF="/documentation/reference_3.1/online/make_ndx.html"><TT>make_ndx</TT></A> to create 
+an <A HREF="/documentation/reference_3.1/online/ndx.html"><TT>.ndx</TT></A> file with only one
 group in it, this is done by typing '<TT>keep #</TT>' in <TT>make_ndx</TT>,
 where '<TT>#</TT>' stands for the one group you want to have. 
 Name the file <TT>index.ndx</TT> (which is the default
@@ -738,32 +835,35 @@ copy the entire contents of the directory you should be able to type
 change the name by editing the Makefile.<br><br>
 
 Now, if you wrote an analysis tool which, in your opinion, adds
-something that is really missing in GROMACS, please 
-<A HREF="mailto:gromacs@gromacs.org">tell us</A> so that all other GROMACS
-users can also benefit from it!
+something that is really missing in GROMACS, please post it on the
+<a href="http://www.gromacs.org/mailing_lists/developers.php">developers 
+mailing list</a> so that all other GROMACS users can also benefit from it!
 <br><br>
 
-<li><A NAME="none">
-<b>My problem isn't mentioned above, and/or none of the solutions seem to work?</b>
-<br><br>
-Check the installation instructions carefully if your problem is related
-to the configuration, building and installation of GROMACS.
-Also try 
-<A HREF="/documentation/reference3.0/online/getting_started.html">"Getting Started"</A> 
-where a guided tour of GROMACS is provided. 
-A quick glance at the <A HREF="/documentation/reference3.0/online/flow.html">flowchart</A>
-will tell you if you missed any essential steps in setting up a run.
-Checking your <A HREF="/documentation/reference3.0/online/mdp.html"><TT>.mdp</TT></A>
-file against our <A HREF="/documentation/reference3.0/online/mdp.html">sample <TT>.mdp</TT>
-file</A> and the <A HREF="/documentation/reference3.0/online/mdp_opt.html">mdp options
+<li><A NAME="none"> <b>My problem isn't mentioned above, and/or none
+of the solutions seem to work?</b> <br><br> Check the installation
+instructions carefully if your problem is related to the
+configuration, building and installation of GROMACS.  Also try <A
+HREF="/documentation/reference_3.1/online/getting_started.html">"Getting
+Started"</A> where a guided tour of GROMACS is provided.  A quick
+glance at the <A
+HREF="/documentation/reference_3.1/online/flow.html">flowchart</A> will
+tell you if you missed any essential steps in setting up a run.
+Checking your <A
+HREF="/documentation/reference_3.1/online/mdp.html"><TT>.mdp</TT></A>
+file against our <A
+HREF="/documentation/reference_3.1/online/mdp.html">sample
+<TT>.mdp</TT> file</A> and the <A
+HREF="/documentation/reference_3.1/online/mdp_opt.html">mdp options
 list</A> might solve a number of potential problems. In general it
-never hurts to read the <A HREF="/documentation/reference3.0/online.html">manual pages</A> of
-all the GROMACS programs you (tried to) use. If all this still leaves
-you with any unanswered questions, <A HREF="mailto:gromacs@gromacs.org">please
-don't hesitate to contact us</A>, or even better - post your question to the mailing lists!
-<br><br>
+never hurts to read the <A
+HREF="/documentation/reference_3.1/online.html">manual pages</A> of all
+the GROMACS programs you (tried to) use. If all this still leaves you
+with any unanswered questions, please post your question to the <a
+href="/mailing_lists/users.php">gmx-users mailing list</a>!  <br><br>
 </ul>
 
+
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>

diff --git a/share/html/online/Makefile.am b/share/html/online/Makefile.am
index 9699361964642b71d8f92d685d3ba9895f6af1aa..655a8edb45e51bd99dc4b9f96349b73cc7af08f3 100644 (file)
--- a/share/html/online/Makefile.am
+++ b/share/html/online/Makefile.am
@@ -7,7 +7,7 @@ onlinedir = ${datadir}/html/online
 online_DATA = \
   dat.html           g_disre.html      g_sorient.html        ndx.html        \
   dlg.html           g_dist.html       g_tcaf.html           ngmx.html       \
-  do_dssp.html       g_dyndom.html     g_traj.html           nmrun.html      \
+  do_dssp.html       g_dyndom.html     g_traj.html           \
   edi.html           g_enemat.html     g_velacc.html         options.html    \
   editconf.html      g_energy.html     genbox.html           out.html        \
   edo.html           g_gyrate.html     genconf.html          pdb.html        \

diff --git a/share/html/online/dat.html b/share/html/online/dat.html
index f43ab189feb5f0978162704cfcb96b4f213ad3a1..bad20661bc846a8527298cf400e6ca56a587fc28 100644 (file)
--- a/share/html/online/dat.html
+++ b/share/html/online/dat.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 Files with the dat file extension contain generic input or output. 
 As it is not possible
@@ -16,6 +16,5 @@ dat of which no format is given.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/dlg.html b/share/html/online/dlg.html
index 540617bea4cded296a5f50078cdba7728b88ef29..7b07bb5e5d7f2c7d207f414984147e68533e7b24 100644 (file)
--- a/share/html/online/dlg.html
+++ b/share/html/online/dlg.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The dlg file format is used as input for the <a href="ngmx.html">ngmx</a>
 trajectory viewer. These files are not meant to be altered bu the end user.
@@ -38,6 +38,5 @@ simple 1 15 37 2 {
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/do_dssp.html b/share/html/online/do_dssp.html
index 630779b58bfcfe83dc433077acf4b6b9b59e91d9..644e4cbb256e4a99b193374fdb1494184b0f8574 100644 (file)
--- a/share/html/online/do_dssp.html
+++ b/share/html/online/do_dssp.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -76,6 +76,5 @@ function of secondary structure type.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/edi.html b/share/html/online/edi.html
index c2e447284a3b9297edbaaa82657f27a229e546f7..0701e296101a354152740dac43ea4645c987ab8f 100644 (file)
--- a/share/html/online/edi.html
+++ b/share/html/online/edi.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 Files with the edi file extension contain information for <a href="mdrun.html">
 mdrun</a> to run Molecular Dynamics with Essential Dynamics constraints.
@@ -18,6 +18,5 @@ output from the programs in the <tt>ESSDYN</tt> menu of the
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/editconf.html b/share/html/online/editconf.html
index 062da22f2362cd2388a8952272e0a68637c294fe..2b3d910346776ce7f16a4317f48441e64d8972e7 100644 (file)
--- a/share/html/online/editconf.html
+++ b/share/html/online/editconf.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>editconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -132,6 +132,5 @@ where <tt>veclen</tt> is the size of the cubic box times sqrt(3)/2.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/edo.html b/share/html/online/edo.html
index 3339c1357b12761cdad8631c06a746d57487ecc1..3f45dea6b3179d287d44c8d37f6e8d03144886b1 100644 (file)
--- a/share/html/online/edo.html
+++ b/share/html/online/edo.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 Files with the edo file extension are generated by <a href="mdrun.html">
 mdrun</a> if Molecular Dynamics is performed with Essential Dynamics 
@@ -20,6 +20,5 @@ utilities like <tt>awk</tt>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/edr.html b/share/html/online/edr.html
index 407837dd4f9daeec077382f8798d0c35d0b931c0..e0c7f50775ba57529e337cd50dfd85185b9bbb4b 100644 (file)
--- a/share/html/online/edr.html
+++ b/share/html/online/edr.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The edr file extension stands for portable energy file. 
 The energies are stored using the xdr protocol.
@@ -16,6 +16,5 @@ See also <a href="g_energy.html">g_energy</a>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/ene.html b/share/html/online/ene.html
index 8f200a65572e96de6f6ccf79c68e8c135f9216d8..2ca52d4ff5345e1afe448e05aba5f4027b266cf3 100644 (file)
--- a/share/html/online/ene.html
+++ b/share/html/online/ene.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The ene file extension stands for binary energy file. It holds the
 energies as generated during your <a href="mdrun.html">mdrun</a>.
@@ -21,6 +21,5 @@ See also <a href="g_energy.html">g_energy</a>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/eneconv.html b/share/html/online/eneconv.html
index 46adec01a6ff73362fbcbee0fc4c02a7f65170f4..64cb314eaa9874d9572fca44bb33d75d5707af7a 100644 (file)
--- a/share/html/online/eneconv.html
+++ b/share/html/online/eneconv.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>eneconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -60,6 +60,5 @@ followed by <tt>-b</tt> and <tt>-e</tt> to select which frames to write.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/eps.html b/share/html/online/eps.html
index 8944312a2ee60fa64c0ebf838d56a8bf863c198f..ed37cc734ed6e8d67959a35c7cdc0ff6faa28686 100644 (file)
--- a/share/html/online/eps.html
+++ b/share/html/online/eps.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The eps file format is not a special GROMACS format, but just a 
 variant of the standard PostScript(tm). A sample eps file as
@@ -19,6 +19,6 @@ of time.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/files.html b/share/html/online/files.html
index 160bec10a77a2f88a35324f7440099ba8ecdd44f..03ee47784edffa14df48c5ba0d64bc03ecdfd08e 100644 (file)
--- a/share/html/online/files.html
+++ b/share/html/online/files.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>File Formats</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Mon 23 Jul 2001</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <dl>
 <dt><h3>Parameter files</h3> 
@@ -121,7 +121,6 @@ density and virials (binary, portable)
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 
 </BODY>
\ No newline at end of file

diff --git a/share/html/online/flow.html b/share/html/online/flow.html
index 0c9516e3085541ef96b10cb6fa779cee5d95ca82..9f8d699b099b343f65023e502bbeb2b761fbcd0d 100644 (file)
--- a/share/html/online/flow.html
+++ b/share/html/online/flow.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>Flow chart</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Mon 23 Jul 2001</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <p>This is a flow chart of a typical GROMACS MD run of a protein
 in a box of water.
@@ -227,7 +227,7 @@ these consist of cycles: grompp -> mdrun.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 
 </BODY>

diff --git a/share/html/online/g87.html b/share/html/online/g87.html
index 96f39ccff784b0042e714cd3df4c2efa9a941d98..30193072fe02c5f6ca0739973d8ee0a4c9ad9fbb 100644 (file)
--- a/share/html/online/g87.html
+++ b/share/html/online/g87.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 This is a simple ASCII format:<br>
 <pre>
 TITLE
@@ -21,6 +21,5 @@ simulations. So, you simply have to remember this stuff.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/g96.html b/share/html/online/g96.html
index 8c8f34f5e4cccea8bbbe950bb11982d21bb3957e..745edd641830a51698f50cfbf23a1964c187aa15 100644 (file)
--- a/share/html/online/g96.html
+++ b/share/html/online/g96.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 
 <p>A file with the g96 extension can be a GROMOS-96 initial/final
 configuration file or a coordinate trajectory file or a combination of both.
@@ -32,7 +32,7 @@ Note that all GROMACS programs can read compressed or g-zipped files.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 
 </body>

diff --git a/share/html/online/g_anaeig.html b/share/html/online/g_anaeig.html
index 0c5af7505b2897ecda800670acfa3099d2d81ac4..16b251da39e4f19b61185470127400237c954b10 100644 (file)
--- a/share/html/online/g_anaeig.html
+++ b/share/html/online/g_anaeig.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anaeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -111,6 +111,5 @@ subspaces are orthogonal.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_analyze.html b/share/html/online/g_analyze.html
index 371f9d9791a07c5d85ba662cadc8611ed10dc3b1..ef9251a4a4075c4ccc3a86e02924624ad4677157 100644 (file)
--- a/share/html/online/g_analyze.html
+++ b/share/html/online/g_analyze.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_analyze</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -104,6 +104,5 @@ zero or negative value are ignored.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_angle.html b/share/html/online/g_angle.html
index 8a7d92a794db4e6e009dbfcd654f0e9bb96ce64f..c226ad91ebc2fb273439d6e2e557403e574a0748 100644 (file)
--- a/share/html/online/g_angle.html
+++ b/share/html/online/g_angle.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_angle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -72,6 +72,5 @@ If this is not the case, the program will crash.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_bond.html b/share/html/online/g_bond.html
index 4c80d39d2444a4f7381d9dde6ef3e675fe561b3a..e94544ef07de4978b11a62aa61783bea5da052d2 100644 (file)
--- a/share/html/online/g_bond.html
+++ b/share/html/online/g_bond.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -58,6 +58,5 @@ the output.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_bundle.html b/share/html/online/g_bundle.html
index 4e9fc74c4ba2b6ba2a4714a84d5d87512806d817..3f127e86d2fe02ada1d669631b9dad009c0a1c55 100644 (file)
--- a/share/html/online/g_bundle.html
+++ b/share/html/online/g_bundle.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bundle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -71,6 +71,5 @@ display the reference axis.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_chi.html b/share/html/online/g_chi.html
index 894642dfc1da28c5600ce85ceabd0013382a5d17..b1ec377efdca2565c68ec8dfc8a441e2eff2070c 100644 (file)
--- a/share/html/online/g_chi.html
+++ b/share/html/online/g_chi.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_chi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -85,6 +85,5 @@ the average omega angle is plotted using color coding.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_cluster.html b/share/html/online/g_cluster.html
index 16eabcf8626e46d5a9b389bf32d2fa09b8ba0a02..50d7e8546a2056d0de128980bb39fcc188ede718 100644 (file)
--- a/share/html/online/g_cluster.html
+++ b/share/html/online/g_cluster.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_cluster</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -112,6 +112,5 @@ for a selected set of clusters (with option <tt>-wcl</tt>, depends on
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_confrms.html b/share/html/online/g_confrms.html
index 6c91e0f865f496a72a8d0861b7cea5cb6ef63d0e..aca7b70cd5e4d777bbb020f0513911ef3514cdea 100644 (file)
--- a/share/html/online/g_confrms.html
+++ b/share/html/online/g_confrms.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_confrms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -46,6 +46,5 @@ the two structures will be written as separate models
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_covar.html b/share/html/online/g_covar.html
index bd4f72c7ccdd39892a4941f1469fa5a72991fb41..453229e8918952a12c735b8348a2a73660fb7451 100644 (file)
--- a/share/html/online/g_covar.html
+++ b/share/html/online/g_covar.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_covar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -68,6 +68,5 @@ written.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_density.html b/share/html/online/g_density.html
index 436169e954b8281d49242f91fb4a1cb3157c29c0..98bf3477a29bdb3f0b1addfe9ba9c69df6769c00 100644 (file)
--- a/share/html/online/g_density.html
+++ b/share/html/online/g_density.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_density</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -62,6 +62,5 @@ partial charge.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_dielectric.html b/share/html/online/g_dielectric.html
index a6e73c3766cd3b95e7ba66d8b52339fe86107bc6..53e81619d39e4b7c7f9f80986982fd83f0e7872b 100644 (file)
--- a/share/html/online/g_dielectric.html
+++ b/share/html/online/g_dielectric.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -75,6 +75,5 @@ plot should be one half of a circle
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_dih.html b/share/html/online/g_dih.html
index 63d604e065ce89aa7f50a1c1a1d53664fc0c5d3d..e242cc2265c77d596db814b6b6742c7d1a316f0d 100644 (file)
--- a/share/html/online/g_dih.html
+++ b/share/html/online/g_dih.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dih</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -52,6 +52,5 @@ conformations sorted according to occupancy.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_dipoles.html b/share/html/online/g_dipoles.html
index 2fd846f3c3113171bf894b6bed6847b12046fd1c..5b6eac99a838edffe974753e8f0be5d27d252eda 100644 (file)
--- a/share/html/online/g_dipoles.html
+++ b/share/html/online/g_dipoles.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -93,6 +93,5 @@ distribution function a maximum of 5.0 will be used.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_disre.html b/share/html/online/g_disre.html
index cd393ea9342c9ea598ba4505651287b6dd77acb5..2a472147015e606a1003ae1a6d7b043cbd5a5787 100644 (file)
--- a/share/html/online/g_disre.html
+++ b/share/html/online/g_disre.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_disre</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -52,6 +52,5 @@ printing.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_dist.html b/share/html/online/g_dist.html
index 49171633a485b238994bfce7af5d26246759c2d0..7837364fd5ee6e67947c67b204b49aef97716c72 100644 (file)
--- a/share/html/online/g_dist.html
+++ b/share/html/online/g_dist.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -46,6 +46,5 @@ and <tt><a href="g_bond.html">g_bond</a></tt>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_dyndom.html b/share/html/online/g_dyndom.html
index 8464e5edba0178cec47c21b0a30fb1fb96fe0277..c50b1066e570be570d382be08be0f1e9cbc4f803 100644 (file)
--- a/share/html/online/g_dyndom.html
+++ b/share/html/online/g_dyndom.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyndom</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -59,6 +59,5 @@ validate the structure.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_enemat.html b/share/html/online/g_enemat.html
index 39e3d1d04f8a4f33deea8cdb33c217bfaa416694..3e38dc55d5b9e360e09d6fbba3d89612f3977a4a 100644 (file)
--- a/share/html/online/g_enemat.html
+++ b/share/html/online/g_enemat.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_enemat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -68,6 +68,5 @@ in the comparison.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_energy.html b/share/html/online/g_energy.html
index 6aedbc04906aba7a207474d20bc0215974358329..606135a2f06c2679a59a3057caee68211387867b 100644 (file)
--- a/share/html/online/g_energy.html
+++ b/share/html/online/g_energy.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_energy</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -105,6 +105,5 @@ the energies must both be calculated from the same trajectory.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_gyrate.html b/share/html/online/g_gyrate.html
index b4a0c2883da2693bd3edf86d64d42042bb201d72..fddeb6d14893498e61b32cb0983fe888fcb2bfec 100644 (file)
--- a/share/html/online/g_gyrate.html
+++ b/share/html/online/g_gyrate.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_gyrate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -43,6 +43,5 @@ and the radii of gyration about the x, y and z axes,as a function of time. The a
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_h2order.html b/share/html/online/g_h2order.html
index a2d4c2c21e088d9acffaab442a1b00e0a2ff1907..60433fc72fe25eca544c25e769ead8037d83eccb 100644 (file)
--- a/share/html/online/g_h2order.html
+++ b/share/html/online/g_h2order.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_h2order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -54,6 +54,5 @@ instead of the angle between the dipole and a box axis.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_hbond.html b/share/html/online/g_hbond.html
index b3ca46b741f671997dcd07a761884ac74e72a737..369d550e96ec9656c7fa25f4b6041b09b4deeea3 100644 (file)
--- a/share/html/online/g_hbond.html
+++ b/share/html/online/g_hbond.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hbond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -101,6 +101,5 @@ each timeframe. This is especially usefull when using <tt>-shell</tt>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_helix.html b/share/html/online/g_helix.html
index a2135371fd5c7849e2e56796b13e718aaf796566..a26de8d1041cdc33449679a5e63a47fef72559af 100644 (file)
--- a/share/html/online/g_helix.html
+++ b/share/html/online/g_helix.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helix</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -78,6 +78,5 @@ atoms only (file rms-ahx.<a href="xvg.html">xvg</a>).<br>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_lie.html b/share/html/online/g_lie.html
index 7b0e80f4e4ef9085a57b0c7719583e17b77c012c..d0210e469ed42a44e543f58fb3c52bab4fd8bd68 100644 (file)
--- a/share/html/online/g_lie.html
+++ b/share/html/online/g_lie.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_lie</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -45,6 +45,5 @@ Coul (A-B) LJ-SR (A-B) etc.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_mdmat.html b/share/html/online/g_mdmat.html
index 372206c2ab2999a17952b9b8f4073ebe0725602a..c0f15629e5a6efde0f1ab98cd74a1bb23dd752a7 100644 (file)
--- a/share/html/online/g_mdmat.html
+++ b/share/html/online/g_mdmat.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mdmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -52,6 +52,5 @@ The output can be processed with <a href="xpm2ps.html">xpm2ps</a> to make a Post
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_mindist.html b/share/html/online/g_mindist.html
index 6a11b6ca99ee2efcca93d137848ea559d32816e6..0dd274cbd5476a58e1f695fbc75fb84a1fda4e02 100644 (file)
--- a/share/html/online/g_mindist.html
+++ b/share/html/online/g_mindist.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mindist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -56,6 +56,5 @@ and <tt><a href="g_bond.html">g_bond</a></tt>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_morph.html b/share/html/online/g_morph.html
index 836a7080851650d5d2fb77d791cd9e075d50e772..0ca2492f029c0a28f6c789b836167133f89f638f 100644 (file)
--- a/share/html/online/g_morph.html
+++ b/share/html/online/g_morph.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_morph</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -55,6 +55,5 @@ read to select what group RMS is computed from.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_msd.html b/share/html/online/g_msd.html
index 9eb90f988dd267077178b77dfe7f68888cc8184e..2beccac9d00863e6128492b1d7fae2179b9e56c1 100644 (file)
--- a/share/html/online/g_msd.html
+++ b/share/html/online/g_msd.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_msd</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -64,6 +64,5 @@ the most useful number.<p>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_nmeig.html b/share/html/online/g_nmeig.html
index 86c8b6e5f2db0d42aaf513c807f60458b42827a6..45f27c7d9688b4a7f89a327525a58df899e7bb61 100644 (file)
--- a/share/html/online/g_nmeig.html
+++ b/share/html/online/g_nmeig.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -46,6 +46,5 @@ An ensemble of structures can be generated from the eigenvectors with
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_nmens.html b/share/html/online/g_nmens.html
index 5b027cea6a62dc9922f59fbda4a733faa85eb55a..a1d8d866b9a6b438147557919281f77b8bd865c4 100644 (file)
--- a/share/html/online/g_nmens.html
+++ b/share/html/online/g_nmens.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmens</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -48,6 +48,5 @@ normal modes are the translational and rotational degrees of freedom.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_order.html b/share/html/online/g_order.html
index 621153fd1fc76f5e014e85b701cb8378b96139c4..4801c05809ca9280b9171939f3bff064cdd961f6 100644 (file)
--- a/share/html/online/g_order.html
+++ b/share/html/online/g_order.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -55,6 +55,5 @@ given.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_potential.html b/share/html/online/g_potential.html
index e65ff23d7ce4111770c97bae63d15c76ca9fed47..b2bea917dc0752e73f0e5be3e3c451cabddcf0d7 100644 (file)
--- a/share/html/online/g_potential.html
+++ b/share/html/online/g_potential.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_potential</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -52,6 +52,5 @@ Compute the electrostatical potential across the box. The potential iscalculated
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_rama.html b/share/html/online/g_rama.html
index fbad15453c6ae28cee2ea0408a3001101b80e1b8..4ff06f964bdc116eb04cd0dbf5b69dc605436886 100644 (file)
--- a/share/html/online/g_rama.html
+++ b/share/html/online/g_rama.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -42,6 +42,5 @@ specific residues.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_rdf.html b/share/html/online/g_rdf.html
index 0f7dc04c40c615e1a7b5d7496c56423e9a1f5012..97331d57dcb73350c9052987f1a36e0784735755 100644 (file)
--- a/share/html/online/g_rdf.html
+++ b/share/html/online/g_rdf.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rdf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -68,6 +68,5 @@ be computed (option <tt>-sq</tt>). The algorithm uses FFT, the gridspacing of wh
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_rms.html b/share/html/online/g_rms.html
index 2e7b326984a2b872f19d34d00f6c787b6c09cdfb..dd3e6e7f9aef186b462ddb43b567cc48846d2bb5 100644 (file)
--- a/share/html/online/g_rms.html
+++ b/share/html/online/g_rms.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -81,6 +81,5 @@ comparison group are considered.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_rmsdist.html b/share/html/online/g_rmsdist.html
index 9f67be7f9f2cb767b15dfbfe4394d2800a9dc10d..f496113bf2d5d52ad39f8e839b7b2ed0cca294d1 100644 (file)
--- a/share/html/online/g_rmsdist.html
+++ b/share/html/online/g_rmsdist.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsdist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -69,6 +69,5 @@ file, including case. Specifying non-sequential atoms is undefined.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_rmsf.html b/share/html/online/g_rmsf.html
index 2015f71c189df8f101e960698e9ad7733690b89d..cdb5201c1bb1567334b8b88e5c923af3a9994e84 100644 (file)
--- a/share/html/online/g_rmsf.html
+++ b/share/html/online/g_rmsf.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -70,6 +70,5 @@ the least.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_rotacf.html b/share/html/online/g_rotacf.html
index 114a901fd33e888f53697c64f335d296ac7f51b7..50799ecb0985e46a253dfc50421d02ddb7b50050 100644 (file)
--- a/share/html/online/g_rotacf.html
+++ b/share/html/online/g_rotacf.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotacf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -66,6 +66,5 @@ to a two parameter exponential
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_saltbr.html b/share/html/online/g_saltbr.html
index 442045389a089f8d84cc48ceb43881d49a2562e2..e1f3f769ca0f194c561458a19fb22c43a95a5efe 100644 (file)
--- a/share/html/online/g_saltbr.html
+++ b/share/html/online/g_saltbr.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_saltbr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -43,6 +43,5 @@ and plus-plus.<a href="xvg.html">xvg</a>, or files for every individual ion-pair
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_sas.html b/share/html/online/g_sas.html
index 48be6df17902048021acc64354cb465487e6141c..f7bd41d2c887d5c07bae1122b226948bed004eda 100644 (file)
--- a/share/html/online/g_sas.html
+++ b/share/html/online/g_sas.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -60,6 +60,5 @@ this can be turned off using the -pbc option.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_sgangle.html b/share/html/online/g_sgangle.html
index 683ef21ac5eb557e5ad6f1f62c40a8a956700c95..fb445e5121ea6aa2e77e7d23256851aa70e8f505 100644 (file)
--- a/share/html/online/g_sgangle.html
+++ b/share/html/online/g_sgangle.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sgangle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -57,6 +57,5 @@ Here is what some of the file options do:<br>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_sorient.html b/share/html/online/g_sorient.html
index 1de81828340145da53f28832ab69256f2849ed5d..ad8b40c9f919117b651f96b837b3804026908713 100644 (file)
--- a/share/html/online/g_sorient.html
+++ b/share/html/online/g_sorient.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -63,6 +63,5 @@ of cos(theta1) and 3cos^2(theta2)-1 as a function of r.<p>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_tcaf.html b/share/html/online/g_tcaf.html
index 711e76cfa6cebc02906cbc34d809187f6f63eceb..59a5417c4c6222e116ccb98417093f9a29eb8832 100644 (file)
--- a/share/html/online/g_tcaf.html
+++ b/share/html/online/g_tcaf.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tcaf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -78,6 +78,5 @@ is very important for obtaining a good fit.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_traj.html b/share/html/online/g_traj.html
index 9798b7d11b22913bc2653750d75d2d99cdead056..facecd58430400cca732b60ab8b1985683370d19 100644 (file)
--- a/share/html/online/g_traj.html
+++ b/share/html/online/g_traj.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_traj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -76,6 +76,5 @@ the <tt>-nojump</tt> option to obtain the correct average coordinates.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/g_velacc.html b/share/html/online/g_velacc.html
index d80d948e7a4cfe7d6c50356e20d3e38278dbf4cc..bf1da5d0a57d21253bad6ff415e4205ad6435f0f 100644 (file)
--- a/share/html/online/g_velacc.html
+++ b/share/html/online/g_velacc.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_velacc</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -53,6 +53,5 @@ of molecule numbers instead of atom numbers.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/genbox.html b/share/html/online/genbox.html
index 5f1f784932b630c1f09bfc25f77a90c16ea29b01..fc789a959e2162867f6ceb76d6b3e6695638fdf7 100644 (file)
--- a/share/html/online/genbox.html
+++ b/share/html/online/genbox.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -97,6 +97,5 @@ line with the total number of solvent molecules in your coordinate file.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/genconf.html b/share/html/online/genconf.html
index be471350a8994da430dbc23a2dcefaea9e0bc6d3..11e37ad8f02163b0c168968fe290a99e48da4cc3 100644 (file)
--- a/share/html/online/genconf.html
+++ b/share/html/online/genconf.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -60,6 +60,5 @@ build the grid.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/genion.html b/share/html/online/genion.html
index 71992b83f489abc43f200cdb919c504199df5919..7d267dc5fd9fff513cd5b578ec7e484965750057 100644 (file)
--- a/share/html/online/genion.html
+++ b/share/html/online/genion.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genion</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -62,6 +62,5 @@ For larger ions, e.g. sulfate we recommended to use <a href="genbox.html">genbox
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/genpr.html b/share/html/online/genpr.html
index 864c36bfc1e56d92cbdd65847e0db67528062d2a..586dbbad905c0df7516197a8a723d475f8ebee41 100644 (file)
--- a/share/html/online/genpr.html
+++ b/share/html/online/genpr.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genpr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -46,6 +46,5 @@ file for the first molecule.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/getting_started.html b/share/html/online/getting_started.html
index 0640a34941e9dc21586efd50c76308f6cf47eb40..d27926ed36ee9b3afb4cd51361a9253cb8aa3e1b 100644 (file)
--- a/share/html/online/getting_started.html
+++ b/share/html/online/getting_started.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Mon 23 Jul 2001</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Contents</H3>
 
@@ -81,8 +81,9 @@ local users in the Groningen MD group it is simply
 '/usr/local/gromacs/<arch>/bin', where <arch>
 is the architecture of your computer. For other users that 
 is probably not the case, contact your local system administrator for
-more information. The GROMACS RPM packages for Linux install binaries
-in '/usr/local/bin', and shared data in '/usr/local/share/gromacs'.
+more information. For instance, the GROMACS RPM packages for Linux 
+install binaries in '/usr/local/bin', and shared data in
+ '/usr/local/share/gromacs' (according to the Linux standard).
 
 <P><H3><A NAME="setup">Setting up your environment</A></H3>
 
@@ -1065,7 +1066,7 @@ vol. 1, p. 211. New York: Freeman, 3 edition.</dd><p>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </BODY>
 </HTML>

diff --git a/share/html/online/gmxcheck.html b/share/html/online/gmxcheck.html
index da391275060f655eb729eb8e07e0ea194a936841..de3da1182f4d1a24a15e766743b9d70997f6095c 100644 (file)
--- a/share/html/online/gmxcheck.html
+++ b/share/html/online/gmxcheck.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxcheck</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -56,6 +56,5 @@ when both <tt>-s1</tt> and <tt>-s2</tt> are supplied.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/gmxdump.html b/share/html/online/gmxdump.html
index 2be9264cc205d32a306f629a920a7e33b4caf9e2..c855dca3608139bff8729150678d2462a38f87cc 100644 (file)
--- a/share/html/online/gmxdump.html
+++ b/share/html/online/gmxdump.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -40,6 +40,5 @@ checking your run input file in case of problems.<p>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/gro.html b/share/html/online/gro.html
index ae7b2171fb8f5ce0db192c02dace24564f661edb..4421b2f5fd30b21168058b0b5189ae572bda94e1 100644 (file)
--- a/share/html/online/gro.html
+++ b/share/html/online/gro.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 
 <p>Files with the gro file extension contain a molecular structure in
 Gromos87 format. gro files can be used as trajectory by simply
@@ -79,6 +79,6 @@ with the same format statement in C.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/grompp.html b/share/html/online/grompp.html
index aa6ec05298ea19504663a82ed5ea0fe4c442613f..4f634d7aa7701d580f84bf89745cb8c13b56f83a 100644 (file)
--- a/share/html/online/grompp.html
+++ b/share/html/online/grompp.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -122,6 +122,5 @@ program.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/hat.html b/share/html/online/hat.html
index e4a01a5369d057bd2f5f0250faa97e25c697b297..f2de2aa0414095cc6ab1f8d844b3ddd76ebb84da 100644 (file)
--- a/share/html/online/hat.html
+++ b/share/html/online/hat.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 Files with the hat file extension contain
 a fourier transform of a spread function used in the PPPM algorithm.
@@ -16,6 +16,6 @@ and read by <a href="mdrun.html">mdrun</a>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/highway.html b/share/html/online/highway.html
index fc86c240816ede0d412b2fe356546f01e23d1f27..ab653005ecb4bfb1a4efb182b76016e81b4117bf 100644 (file)
--- a/share/html/online/highway.html
+++ b/share/html/online/highway.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>highway</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -40,6 +40,5 @@ number of crashes. Nice for a background CPU-eater
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/itp.html b/share/html/online/itp.html
index 5e62045e1f762bc68d1071056cde7e4cf445972f..9c5cd456256a21c9bab78a14ed1db555f3eedd80 100644 (file)
--- a/share/html/online/itp.html
+++ b/share/html/online/itp.html
@@ -5,14 +5,13 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The itp file extension stands for include toplogy. These files are included in topology files ( with the <a href="top.html"><tt>top</tt></a> extension )
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/log.html b/share/html/online/log.html
index e5b483d155a5a8512d2eff0bfd10a49111532cef..74db4fd9a3c60ad7a780bf43e4618d0269e21f02 100644 (file)
--- a/share/html/online/log.html
+++ b/share/html/online/log.html
@@ -5,15 +5,15 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 Logfiles are generated by some GROMACS programs and are usually in
 human-readable format. Use <tt>more logfile</tt>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/m2p.html b/share/html/online/m2p.html
index 6f81363d9f4645bd27f514893470587144707fca..88b72d1530c8cf624a9be894a5c914dbc346feb0 100644 (file)
--- a/share/html/online/m2p.html
+++ b/share/html/online/m2p.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The m2p file format contains input options for the 
 <a href="xpm2ps.html">xpm2ps</a> program. All of these options
@@ -54,6 +54,5 @@ y-tickfont               = Helvetica
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/make_ndx.html b/share/html/online/make_ndx.html
index 91b1d47080a3650f5b2bb38dd4e534d11daf9bc5..a5e95658f594bd05c0e04393eafb8ee628ee37b8 100644 (file)
--- a/share/html/online/make_ndx.html
+++ b/share/html/online/make_ndx.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_ndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -45,6 +45,5 @@ The atom numbering in the editor and the index file starts at 1.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/map.html b/share/html/online/map.html
index 25aa45aba695b694311be9e89bd9c136aba839c1..8e020520309b56cf2ed6cba5fbf684bb751b8830 100644 (file)
--- a/share/html/online/map.html
+++ b/share/html/online/map.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 This file maps matrix data to RGB values which is used by the 
 <a href="do_dssp.html">do_dssp</a> program.<p>
@@ -33,6 +33,5 @@ I     5-Helix         1.0       0.6     0.0
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/mdp.html b/share/html/online/mdp.html
index 4dd3874402e47f9a08cdeaab56b346134742154c..0b50975f36368290cae5c90d1dbca295c365a479 100644 (file)
--- a/share/html/online/mdp.html
+++ b/share/html/online/mdp.html
@@ -6,9 +6,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>.  </P>
 
 <P> Below is a sample mdp file.
@@ -243,6 +243,5 @@ userreal4                = 0
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html
index 60ebc6523c53895ba63bbde46bfc3bdc88bd8e2f..96b4b45d7199bbf4cfa00179f055ea5490f25118 100644 (file)
--- a/share/html/online/mdp_opt.html
+++ b/share/html/online/mdp_opt.html
@@ -10,7 +10,7 @@
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 3.1<br>
-Mon 23 Jul 2001</B></td></tr></TABLE>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 
 <!-- 
@@ -994,7 +994,7 @@ reals to your subroutine. Check the inputrec definition in
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </BODY>
 </HTML>

diff --git a/share/html/online/mdrun.html b/share/html/online/mdrun.html
index 3913954df161226c536f30b231dedfe0da0bce3b..95018e461f5f72d43f07720f19877765763c4d78 100644 (file)
--- a/share/html/online/mdrun.html
+++ b/share/html/online/mdrun.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -122,6 +122,5 @@ and parallel independent simulations.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/mk_angndx.html b/share/html/online/mk_angndx.html
index 1b2a8cb3d74ccf1784915c0d497d0ee20de8587d..c219fbd93e8492b48a4c1523bb9c2debc924b38a 100644 (file)
--- a/share/html/online/mk_angndx.html
+++ b/share/html/online/mk_angndx.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mk_angndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -37,6 +37,5 @@ definitions of the angles, dihedrals etc.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/mtx.html b/share/html/online/mtx.html
index 84f2558a7f78300e2e064c92447962bcbfee0036..a0a1abd03f21730b3d1fa02cca6adfb8f79f8dd5 100644 (file)
--- a/share/html/online/mtx.html
+++ b/share/html/online/mtx.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 Files with the mtx file extension contain a matrix.
 The file format is identical to the <a href="trj.html">trj</a> format.
@@ -17,6 +17,6 @@ which are produced with <a href="nmrun.html">nmrun</a> and read by
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/ndx.html b/share/html/online/ndx.html
index f73b48beaa0259950bed815c17facad7f3c1c0a0..c29dcab1927d90217e76e7c448a173c1602200fc 100644 (file)
--- a/share/html/online/ndx.html
+++ b/share/html/online/ndx.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The GROMACS index file (usually called index.ndx) contains some
 user definable sets of atoms. The file can be read by
@@ -39,6 +39,5 @@ An index file generation tool is available: <a href=make_ndx.html>make_ndx</a>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/ngmx.html b/share/html/online/ngmx.html
index 7c327f24be4f73bcce9129c3ab32e8a9612f4f1b..0328ea206192b24caf6792aa92b1f428dc51c55b 100644 (file)
--- a/share/html/online/ngmx.html
+++ b/share/html/online/ngmx.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>ngmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -56,6 +56,5 @@ Some of the more common X command line options can be used:<br>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/nmrun.html b/share/html/online/nmrun.html
deleted file mode 100644 (file)
index c34602f..0000000
--- a/share/html/online/nmrun.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>nmrun</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>nmrun</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
-<HR>
-<H3>Description</H3>
-<p>
-nmrun builds a Hessian matrix from single conformation.
-For usual Normal Modes-like calculations, make sure that
-the structure provided is properly energy-minimised.
-The generated matrix can be diagonalized by <a href="g_nmeig.html">g_nmeig</a>.
-<P>
-<H3>Files</H3>
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-m</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Output </TD><TD> Hessian matrix </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">      nm.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
-</TABLE>
-<P>
-<H3>Other options</H3>
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of nodes, must be the same as used for <a href="grompp.html">grompp</a> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Verbose mode </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Write a compact log file </TD></TD>
-</TABLE>
-<P>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
-</div>
-</BODY>

diff --git a/share/html/online/out.html b/share/html/online/out.html
index 951a907b0c793abc2bf24b8f6a7ab1777ec572c6..721b3669ac421e192c5327492132578d46757278 100644 (file)
--- a/share/html/online/out.html
+++ b/share/html/online/out.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 Files with the out file extension contain generic output. As it is not possible
 to categorise all data file formats, GROMACS has a generic file format called
@@ -15,6 +15,6 @@ out of which no format is given.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/pdb.html b/share/html/online/pdb.html
index 057c181761bf2cab804d6627c494a57ecb91b679..c2a3d72b4efd04be15a12d1863ae5bd06d3af1c3 100644 (file)
--- a/share/html/online/pdb.html
+++ b/share/html/online/pdb.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 
 Files with the <a href="pdb.html">.pdb</a> extension are molecular
@@ -46,7 +46,7 @@ can be found on the <A HREF="../links.html">Links page</A>.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 
 </body>

diff --git a/share/html/online/pdb2gmx.html b/share/html/online/pdb2gmx.html
index 5857f8a9c676f45121880e93d0f21b3f6761c519..5ae3ab0546490d112da3d375efe0e24e0454d88d 100644 (file)
--- a/share/html/online/pdb2gmx.html
+++ b/share/html/online/pdb2gmx.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>pdb2gmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -119,6 +119,5 @@ Reference Feenstra et al., J. Comput. Chem. 20, 786 (1999).
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/protonate.html b/share/html/online/protonate.html
index 705dd812dce49b677a9029bde0612cbd99bcdd4a..1de58880d7002ca4096f80295aec5927cb8162a8 100644 (file)
--- a/share/html/online/protonate.html
+++ b/share/html/online/protonate.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -50,6 +50,5 @@ should correspond to the <b>protonated</b> state.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/rtp.html b/share/html/online/rtp.html
index 8559d22aaa1e0406c1e04d34c807c17e215ff367..5b75f660b3d5ec9cee1c28f71581ab7d545f7049 100644 (file)
--- a/share/html/online/rtp.html
+++ b/share/html/online/rtp.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The rtp file extension stands for residue toplogy. 
 Such a file is needed by <a href="pdb2gmx.html">pdb2gmx</a>
@@ -90,6 +90,6 @@ A sample is included below.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/tex.html b/share/html/online/tex.html
index 01a6808713147fcddb925e7839265828e4458cd8..c1c8129a04b9ed2a2e92d5c58a82735b778dc2c0 100644 (file)
--- a/share/html/online/tex.html
+++ b/share/html/online/tex.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 We use <b>LaTeX</b> for <i>document</i> processing. 
 Although the input is not so
@@ -21,6 +21,6 @@ user friendly, it has some  advantages over <i>word</i> processors.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/top.html b/share/html/online/top.html
index 8a70c2b534b192c2db3235476b32d4980ea3dd91..0eaf1ce549511e8fd5dbb75472b53132977f62cb 100644 (file)
--- a/share/html/online/top.html
+++ b/share/html/online/top.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The top file extension stands for topology. It is an ascii file which is 
 read by <a href="grompp.html">grompp</a> which processes it
@@ -102,6 +102,5 @@ SOL 1000
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/tpa.html b/share/html/online/tpa.html
index 8ebf8ea2fe11bed419ae7a2ff3605243c038af76..ca8e92fc90475405ab64ece599d744c2479157d5 100644 (file)
--- a/share/html/online/tpa.html
+++ b/share/html/online/tpa.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The tpa file extension stands for binary run input file. This file contains 
 the starting structure of your simulation, The molecular topology and 
@@ -29,7 +29,7 @@ You can also compare two tpa files using:
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 </body>

diff --git a/share/html/online/tpb.html b/share/html/online/tpb.html
index 1eb5fa317a2f093377b81b3de117b7ec055a26fc..4cf43632a17e0ff0229f4b6db7e095e3d349a921 100644 (file)
--- a/share/html/online/tpb.html
+++ b/share/html/online/tpb.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The tpb file extension stands for binary run input file. This file contains 
 the starting structure of your simulation, The molecular topology and 
@@ -29,7 +29,7 @@ You can also compare two tpb files using:
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 </body>

diff --git a/share/html/online/tpbconv.html b/share/html/online/tpbconv.html
index d18ad09c0b422f83d79859731ae16cb0f1d61a3c..446686336ca65c236d0ba516d43ce0f37b8fdeee 100644 (file)
--- a/share/html/online/tpbconv.html
+++ b/share/html/online/tpbconv.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>tpbconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -53,6 +53,5 @@ using the LIE (Linear Interactio Energy) method.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/tpr.html b/share/html/online/tpr.html
index e250945edb86e4e250dcea2d3c26ad5f8b55aba5..40ffba7a6ddb4c602180c97d3c2f7442c19f269f 100644 (file)
--- a/share/html/online/tpr.html
+++ b/share/html/online/tpr.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 The tpr file extension stands for portable binary run input file. This file 
 contains  the starting structure of your simulation, the molecular topology 
@@ -30,6 +30,5 @@ You can also compare two tpr files using:
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/trj.html b/share/html/online/trj.html
index da6e4821f481c01f00210737ba2534cd563af6cc..be4fd10d59b14ce37eb979ea256829eced7bd355 100644 (file)
--- a/share/html/online/trj.html
+++ b/share/html/online/trj.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 Files with the trj file extension contain the trajectory of a simulation. 
 In this file all the coordinates, velocities, forces and energies are 
@@ -30,6 +30,6 @@ frames etc.) using:
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/trjcat.html b/share/html/online/trjcat.html
index 98f71da47cccbcfefe55960d8c39efba5351387d..e68bd125a505098a0ba1d657d446357d81cc7f94 100644 (file)
--- a/share/html/online/trjcat.html
+++ b/share/html/online/trjcat.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjcat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -49,6 +49,5 @@ together without removal of frames with identical time stamps.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/trjconv.html b/share/html/online/trjconv.html
index 2817e7ba568862fadd0a64640cddfa78104dd03c..7490b6de6214586bcea6998ef464c890a36b7c93 100644 (file)
--- a/share/html/online/trjconv.html
+++ b/share/html/online/trjconv.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -148,6 +148,5 @@ one specific time from your trajectory.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/trjorder.html b/share/html/online/trjorder.html
index 0e44f4a800bff92298f72cc0e5357b6157f4e5ae..5101de058cff789c827e95157161630ac8de9b1f 100644 (file)
--- a/share/html/online/trjorder.html
+++ b/share/html/online/trjorder.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -53,6 +53,5 @@ with any Gromacs program to analyze the n closest waters.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/trr.html b/share/html/online/trr.html
index a11a2ce567cc0e2d5b3f15ebd9bb948f8785b9f3..108ff049d2c13925a9bde604a5e375c3d1e9ea69 100644 (file)
--- a/share/html/online/trr.html
+++ b/share/html/online/trr.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <h3>Description</h3>
 Files with the trr file extension contain the trajectory of a simulation. 
 In this file all the coordinates, velocities, forces and energies are 
@@ -30,6 +30,6 @@ frames etc.) using:
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+
 </div>
 </body>

diff --git a/share/html/online/wheel.html b/share/html/online/wheel.html
index cf00a4788d1867ede48b7831ee42a12f5192a350..f2915f7b13e52e29cea52d2ddcae394133c4ec1f 100644 (file)
--- a/share/html/online/wheel.html
+++ b/share/html/online/wheel.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -39,6 +39,5 @@ the number of residues and each consecutive line contains a residuename.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/x2top.html b/share/html/online/x2top.html
index 8680d71d6a3d4518a1b2af15d1e20017dea9e377..a25ab32647d9b12d5f8b7c685ea28677d2245091 100644 (file)
--- a/share/html/online/x2top.html
+++ b/share/html/online/x2top.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -63,6 +63,5 @@ command line options.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/xmdrun.html b/share/html/online/xmdrun.html
deleted file mode 100644 (file)
index e7b5132..0000000
--- a/share/html/online/xmdrun.html
+++ /dev/null
@@ -1,117 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>xmdrun</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xmdrun</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
-<HR>
-<H3>Description</H3>
-<p>
-xmdrun is the experimental MD program. New features are tested in this
-program before being implemented in the default <a href="mdrun.html">mdrun</a>. Currently under
-investigation are: polarizibility, glass simulations, 
-Free energy perturbation, X-Ray bombardments
-and parallel independent simulations.It reads the run input file (<tt>-s</tt>) and distributes the
-topology over nodes if needed. The coordinates are passed
-around, so that computations can begin.
-First a neighborlist is made, then the forces are computed.
-The forces are globally summed, and the velocities and
-positions are updated. If necessary shake is performed to constrain
-bond lengths and/or bond angles.
-Temperature and Pressure can be controlled using weak coupling to a
-bath.<p>
-<a href="mdrun.html">mdrun</a> produces at least three output file, plus one log file
-(<tt>-g</tt>) per node.
-The trajectory file (<tt>-o</tt>), contains coordinates, velocities and
-optionally forces.
-The structure file (<tt>-c</tt>) contains the coordinates and
-velocities of the last step.
-The energy file (<tt>-e</tt>) contains energies, the temperature,
-pressure, etc, a lot of these things are also printed in the log file
-of node 0.
-Optionally coordinates can be written to a compressed trajectory file
-(<tt>-x</tt>).<p>
-When running in parallel with PVM or an old version of MPI the
-<tt>-np</tt> option must be given to indicate the number of
-nodes.<p>
-The option <tt>-dgdl</tt> is only used when free energy perturbation is
-turned on.<p>
-With <tt>-rerun</tt> an input trajectory can be given for which 
-forces and energies will be (re)calculated. Neighbor searching will be
-performed for every frame, unless <tt>nstlist</tt> is zero
-(see the <tt>.<a href="mdp.html">mdp</a></tt> file).<p>
-ED (essential dynamics) sampling is switched on by using the <tt>-ei</tt>
-flag followed by an <tt>.<a href="edi.html">edi</a></tt> file.
-The <tt>.<a href="edi.html">edi</a></tt> file can be produced using options in the essdyn
-menu of the WHAT IF program. <a href="mdrun.html">mdrun</a> produces a <tt>.<a href="edo.html">edo</a></tt> file that
-contains projections of positions, velocities and forces onto selected
-eigenvectors.<p>
-The -table option can be used to pass <a href="mdrun.html">mdrun</a> a formatted table with
-user-defined potential functions. The file is read from either the
-current directory or from the GMXLIB directory. A number of preformatted
-tables are presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12
-Lennard Jones potentials with normal Coulomb.<p>
-The options <tt>-pi</tt>, <tt>-po</tt>, <tt>-pd</tt>, <tt>-pn</tt> are used
-for potential of mean force calculations and umbrella sampling.
-See manual.<p>
-When <a href="mdrun.html">mdrun</a> receives a TERM signal, it will set nsteps to the current
-step plus one. When <a href="mdrun.html">mdrun</a> receives a USR1 signal, it will set nsteps
-to the next multiple of nstxout after the current step.
-In both cases all the usual output will be written to file.
-When running with MPI, a signal to one of the <a href="mdrun.html">mdrun</a> processes
-is sufficient, this signal should not be sent to mpirun or
-the <a href="mdrun.html">mdrun</a> process that is the parent of the others.
-<P>
-<H3>Files</H3>
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html">    traj.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> confout.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    ener.edr</a></tt> </TD><TD> Output </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">      md.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-dgdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    dgdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html">     sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html">     sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">    wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">     bam.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-devout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">deviatie.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html">    pull.ppa</a></tt> </TD><TD> Input, Opt. </TD><TD> Pull parameters </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html"> pullout.ppa</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull parameters </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdo.html">    pull.pdo</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull data output </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">    pull.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-</TABLE>
-<P>
-<H3>Other options</H3>
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Use dialog box GUI to edit command line options </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of nodes, must be the same as used for <a href="grompp.html">grompp</a> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Be loud and noisy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Write a compact log file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]multi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Do multiple simulations in parallel (only with -np &gt; 1) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]glas</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Do glass simulation with special long range corrections </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
-</TABLE>
-<P>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
-</div>
-</BODY>

diff --git a/share/html/online/xpm.html b/share/html/online/xpm.html
index 85a0a7eba319a36311d772eccc458471be14bd33..e7873e151df2265191cedf1443be14409e7a4a29 100644 (file)
--- a/share/html/online/xpm.html
+++ b/share/html/online/xpm.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The GROMACS xpm file format is compatible with the XPixMap format
 and is used for storing matrix data.
@@ -74,6 +74,5 @@ static char * gv_xpm[] = {
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/xpm2ps.html b/share/html/online/xpm2ps.html
index 90c4bbf8c7127e83d40d6320b586389ebaa8da39..72ec8636a4a2c23d11cdbc7e5f62e3b8765a29a8 100644 (file)
--- a/share/html/online/xpm2ps.html
+++ b/share/html/online/xpm2ps.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xpm2ps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -81,6 +81,5 @@ the <tt>-<a href="xpm.html">xpm</a></tt> option.
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/xrama.html b/share/html/online/xrama.html
index 3935542923e6d8a5a7297c61b4a417f2aa291ffa..66a1747454f91a0cda31cc2512e8be65d9b49c3c 100644 (file)
--- a/share/html/online/xrama.html
+++ b/share/html/online/xrama.html
@@ -9,8 +9,8 @@
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xrama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
+Thu 28 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -40,6 +40,5 @@ Some of the more common X command line options can be used:<br>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </BODY>

diff --git a/share/html/online/xtc.html b/share/html/online/xtc.html
index c3a43040060f5836a90dfe6313540af3e7a2a4b4..cf1e6ed14e70e0e7b86d1f11cc647361bf451647 100644 (file)
--- a/share/html/online/xtc.html
+++ b/share/html/online/xtc.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 The xtc format is a <b>portable</b> format for trajectories.
 It uses the <i>xdr</i> routines for writing and reading
@@ -107,6 +107,5 @@ The source for this test can be found in file
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/share/html/online/xvg.html b/share/html/online/xvg.html
index 713ca88a451fbf0b6cfedfc210b6efd8045e35e8..30c3bfdb56bb439da72bc1c8cde73ebe47faf1c9 100644 (file)
--- a/share/html/online/xvg.html
+++ b/share/html/online/xvg.html
@@ -5,9 +5,9 @@
 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
 <TR>
 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Tue 15 May 2001</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Wed 27 Feb 2002</B></TR></TABLE></CENTER><HR>
 <H3>Description</H3>
 Almost all output from GROMACS analysis tools is ready as input for
 Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also
@@ -20,6 +20,5 @@ A sample Grace session with GROMACS data is shown below.<br><br>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </div>
 </body>

diff --git a/src/gmxlib/detectcpu.c b/src/gmxlib/detectcpu.c
index 32387033314167e38f02a7c1e7dfaedb8753f69e..b440bcb827169aa60cd544f7e4c67cecbfcbf2c8 100644 (file)
--- a/src/gmxlib/detectcpu.c
+++ b/src/gmxlib/detectcpu.c
@@ -74,16 +74,8 @@ static void sigill_handler(int n)
  * but make sure we use the result so it is not optimized away.
  * We use the oppurtunity to set the control register to non-java mode.
  */
-static void check_altivec(void)
-{
-#ifdef __VEC__
-  vector unsigned short vsr1,vsr2;
-  vsr1=vec_mfvscr();
-  vsr2=(vector unsigned short)vec_sl(vec_splat_u32(1),vec_splat_u32(16));
-  vsr1=vec_or(vsr1,vsr2);
-  vec_mtvscr(vsr1);
-#endif
-}
+void check_altivec(void);
+
 
 static int detect_altivec(FILE *log)
 {
@@ -98,16 +90,14 @@ static int detect_altivec(FILE *log)
   /* if we got here, its ppc! */
   cpuflags |= PPC_CPU;
 
-#ifdef __VEC__
   if(log)
     fprintf(log,"\nTesting PPC Altivec support...\n");
   success=1;
   signal(SIGILL,sigill_handler);
   setjmp(mainloop); /* return to this point if we get SIGILL */
-  if(success)
-    check_altivec();
-  
   if(success) {
+    check_altivec();
+
     cpuflags |= PPC_ALTIVEC_SUPPORT;
     if(log)
       fprintf(log,"CPU supports Altivec.\n"
@@ -116,7 +106,7 @@ static int detect_altivec(FILE *log)
     if(log)
       fprintf(log,"No Altivec support found.\n");
   }
-#endif
+
   return cpuflags;
 }
 #endif /* PPC_ALTIVEC */
@@ -316,7 +306,7 @@ static int detect_x86(FILE *log)
 int detect_cpu(FILE *log)
 {
   int cpuflags=0;
-  
+
 #ifdef USE_PPC_ALTIVEC
   cpuflags=detect_altivec(log);
 #elif (defined USE_X86_SSE_AND_3DNOW || defined USE_X86_SSE2)

diff --git a/src/gmxlib/inner_altivec.c b/src/gmxlib/inner_altivec.c
index 2903afa7fbc6dc3864db032115e049535d46b4b4..0822c765aba6edee94bc0c9dc66b43e2ffee1a8a 100644 (file)
--- a/src/gmxlib/inner_altivec.c
+++ b/src/gmxlib/inner_altivec.c
@@ -33,6 +33,18 @@ static char *SRCID_inner_altivec_c = "$Id$";
 #include <ppc_altivec.h>
 
 #include<stdio.h>
+
+
+void check_altivec(void)
+{
+  vector unsigned short vsr1,vsr2;
+  vsr1=vec_mfvscr();
+  vsr2=(vector unsigned short)vec_sl(vec_splat_u32(1),vec_splat_u32(16));
+  vsr1=vec_or(vsr1,vsr2);
+  vec_mtvscr(vsr1);
+}
+
+
 void inl0100_altivec(
             int nri,
             int iinr[],

diff --git a/src/gmxlib/wman.c b/src/gmxlib/wman.c
index 8dcb5bdb541e4e47b67179be963e198ede63b94f..77cad2e43b079de732101c18942bf01e80a09efb 100644 (file)
--- a/src/gmxlib/wman.c
+++ b/src/gmxlib/wman.c
@@ -522,8 +522,6 @@ static void write_htmlman(FILE *out,
   fprintf(out,"<hr>\n<div ALIGN=RIGHT>\n");
   fprintf(out,"<font size=\"-1\"><a href=\"http://www.gromacs.org\">"
          "http://www.gromacs.org</a></font><br>\n");
-  fprintf(out,"<font size=\"-1\"><a href=\"mailto:gromacs@gromacs.org\">"
-         "gromacs@gromacs.org</a></font><br>\n");
   fprintf(out,"</div>\n");
   fprintf(out,"</BODY>\n");
 }

diff --git a/src/mdlib/Makefile.am b/src/mdlib/Makefile.am
index eeeed76cca6e1014742dd5b2ca17bddfb01ba1ea..fe02298bae06f926d419ffbc831f902b66afe23a 100644 (file)
--- a/src/mdlib/Makefile.am
+++ b/src/mdlib/Makefile.am
@@ -24,7 +24,7 @@ libmd@LIBSUFFIX@_la_SOURCES = \
        splittop.c      tables.c        tgroup.c        \
        update.c        vcm.c           wnblist.c       \
        poisson.h       splittop.h      wnblist.h       \
-       pull-internal.h
+       pull_internal.h
 
 EXTRA_libmd@LIBSUFFIX@_la_SOURCES = \
        csettle.c       clincs.c        \