Added tip5p to the list of watermodels in some FF.

Added support for flexible tip5p to OPLSAA and parameters
were taken from the Amber/Charmm tip5p.itp files.

There are, however, various problems with that water model.
This commit doesn't resolve them so the bug report below
will need to be followed up at later stage.

watermodels.dat now includes a note about these issues
and refers users to the redmine report.

Refs #1348.

Change-Id: I3adaae21f35efbb4240716e91f1bb5d256c8853e

diff --git a/share/top/amber03.ff/tip5p.itp b/share/top/amber03.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amber03.ff/tip5p.itp
+++ b/share/top/amber03.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amber03.ff/watermodels.dat b/share/top/amber03.ff/watermodels.dat
index 420808db5e5779b24161f08d306c6dda18d5ec8e..7e4956a7e9a47dd4fafbf390fb65446eade24058 100644 (file)
--- a/share/top/amber03.ff/watermodels.dat
+++ b/share/top/amber03.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/amber94.ff/tip5p.itp b/share/top/amber94.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amber94.ff/tip5p.itp
+++ b/share/top/amber94.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amber94.ff/watermodels.dat b/share/top/amber94.ff/watermodels.dat
index 420808db5e5779b24161f08d306c6dda18d5ec8e..7e4956a7e9a47dd4fafbf390fb65446eade24058 100644 (file)
--- a/share/top/amber94.ff/watermodels.dat
+++ b/share/top/amber94.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/amber96.ff/tip5p.itp b/share/top/amber96.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amber96.ff/tip5p.itp
+++ b/share/top/amber96.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amber96.ff/watermodels.dat b/share/top/amber96.ff/watermodels.dat
index 420808db5e5779b24161f08d306c6dda18d5ec8e..7e4956a7e9a47dd4fafbf390fb65446eade24058 100644 (file)
--- a/share/top/amber96.ff/watermodels.dat
+++ b/share/top/amber96.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/amber99.ff/tip5p.itp b/share/top/amber99.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amber99.ff/tip5p.itp
+++ b/share/top/amber99.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amber99.ff/watermodels.dat b/share/top/amber99.ff/watermodels.dat
index 420808db5e5779b24161f08d306c6dda18d5ec8e..7e4956a7e9a47dd4fafbf390fb65446eade24058 100644 (file)
--- a/share/top/amber99.ff/watermodels.dat
+++ b/share/top/amber99.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/amber99sb-ildn.ff/tip5p.itp b/share/top/amber99sb-ildn.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amber99sb-ildn.ff/tip5p.itp
+++ b/share/top/amber99sb-ildn.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amber99sb-ildn.ff/watermodels.dat b/share/top/amber99sb-ildn.ff/watermodels.dat
index 420808db5e5779b24161f08d306c6dda18d5ec8e..7e4956a7e9a47dd4fafbf390fb65446eade24058 100644 (file)
--- a/share/top/amber99sb-ildn.ff/watermodels.dat
+++ b/share/top/amber99sb-ildn.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/amber99sb.ff/tip5p.itp b/share/top/amber99sb.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amber99sb.ff/tip5p.itp
+++ b/share/top/amber99sb.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amber99sb.ff/watermodels.dat b/share/top/amber99sb.ff/watermodels.dat
index 66f8fabc0b116a10ed35a2b5ba60fd2b3a68836d..fa5b9442f647acf64c00e4bdcfdbe5a8062f0920 100644 (file)
--- a/share/top/amber99sb.ff/watermodels.dat
+++ b/share/top/amber99sb.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald, recommended 
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/amberGS.ff/tip5p.itp b/share/top/amberGS.ff/tip5p.itp
index c3120b0ed1e9345c044dc59215e7e5b55876c178..007b57acda9154e630a58e5e43178ddf7fee7b40 100644 (file)
--- a/share/top/amberGS.ff/tip5p.itp
+++ b/share/top/amberGS.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/amberGS.ff/watermodels.dat b/share/top/amberGS.ff/watermodels.dat
index 420808db5e5779b24161f08d306c6dda18d5ec8e..7e4956a7e9a47dd4fafbf390fb65446eade24058 100644 (file)
--- a/share/top/amberGS.ff/watermodels.dat
+++ b/share/top/amberGS.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p    TIP3P     TIP 3-point, recommended
 tip4p    TIP4P     TIP 4-point
 tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
+tip5p    TIP5P     TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc      SPC       simple point charge
 spce     SPC/E     extended simple point charge

diff --git a/share/top/charmm27.ff/tip5p.itp b/share/top/charmm27.ff/tip5p.itp
index d5e92ffd61480223335e135ff9129a0fc3bbf33d..d13477c90f5eeac1c0efa5061a58f832d2827c48 100644 (file)
--- a/share/top/charmm27.ff/tip5p.itp
+++ b/share/top/charmm27.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname      nrexcl
 SOL            2

diff --git a/share/top/charmm27.ff/watermodels.dat b/share/top/charmm27.ff/watermodels.dat
index 72f00cd5db86072aef34ef3cf47f5cbfba2fe856..5446473cdee132eadedde36c29193336919ab077 100644 (file)
--- a/share/top/charmm27.ff/watermodels.dat
+++ b/share/top/charmm27.ff/watermodels.dat
@@ -1,5 +1,6 @@
 tip3p   TIP3P   TIP 3-point, recommended
 tip4p   TIP4P   TIP 4-point
 tips3p  TIPS3P  CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS)
+tip5p   TIP5P   TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc     SPC     simple point charge
 spce    SPC/E   extended simple point charge

diff --git a/share/top/oplsaa.ff/tip5p.itp b/share/top/oplsaa.ff/tip5p.itp
index 02b8c67fa5f17e883d3443b9d537492796a153c5..22418b5f6239700d09341a9e36c86493c1569aad 100644 (file)
--- a/share/top/oplsaa.ff/tip5p.itp
+++ b/share/top/oplsaa.ff/tip5p.itp
@@ -1,3 +1,8 @@
+; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
+;
+; Note that there are various issues with tip5p and the different forcefields.
+; Discussion is here: http://redmine.gromacs.org/issues/1348
+
 [ moleculetype ]
 ; molname       nrexcl
 SOL             2
@@ -10,10 +15,25 @@ SOL             2
 4       opls_120     1       SOL             LP1             1      -0.241
 5       opls_120     1       SOL             LP2             1      -0.241
 
+#ifndef FLEXIBLE
+
 [ settles ]
 ; i     funct   doh     dhh
 1       1       0.09572 0.15139
 
+#else
+
+[ bonds ]
+; i     j       funct   length  force.c.
+1       2       1       0.09572 502416.0 0.09572        502416.0
+1       3       1       0.09572 502416.0 0.09572        502416.0
+
+[ angles ]
+; i     j       k       funct   angle   force.c.
+2       1       3       1       104.52  628.02  104.52  628.02
+
+#endif
+
 [ virtual_sites3 ]
 ; The position of the virtual site is computed as follows:
 ;

diff --git a/share/top/oplsaa.ff/watermodels.dat b/share/top/oplsaa.ff/watermodels.dat
index 513bcae0d6222a9e18396176f495b23dde4400b3..cf93b0691c63d346869d73f24009af585d689c8e 100644 (file)
--- a/share/top/oplsaa.ff/watermodels.dat
+++ b/share/top/oplsaa.ff/watermodels.dat
@@ -1,5 +1,5 @@
 tip4p   TIP4P  TIP 4-point, recommended
 tip3p   TIP3P  TIP 3-point
-tip5p   TIP5P  TIP 5-point
+tip5p   TIP5P  TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 spc     SPC    simple point charge
 spce    SPC/E  extended simple point charge