Add TNG to trjconv doc and more details about TNG selections.

[alexxy/gromacs.git] / src / gromacs / tools / trjconv.cpp

diff --git a/src/gromacs/tools/trjconv.cpp b/src/gromacs/tools/trjconv.cpp
index 67eb02938ad83aac3a172aff3c86c92eaa09e931..132c862620664606598fafabfb18e405eae4f787 100644 (file)
--- a/src/gromacs/tools/trjconv.cpp
+++ b/src/gromacs/tools/trjconv.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -242,8 +242,8 @@ int gmx_trjconv(int argc, char* argv[])
         "[PAR]",
 
         "The following formats are supported for input and output:",
-        "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt]",
-        "and [REF].pdb[ref].",
+        "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt],",
+        "[REF].pdb[ref] and [REF].tng[ref].",
         "The file formats are detected from the file extension.",
         "The precision of the [REF].xtc[ref] output is taken from the",
         "input file for [REF].xtc[ref], [REF].gro[ref] and [REF].pdb[ref],",
@@ -253,7 +253,7 @@ int gmx_trjconv(int argc, char* argv[])
         "output can be single or double precision, depending on the precision",
         "of the [THISMODULE] binary.",
         "Note that velocities are only supported in",
-        "[REF].trr[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
+        "[REF].trr[ref], [REF].tng[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
 
         "Option [TT]-sep[tt] can be used to write every frame to a separate",
         "[TT].gro, .g96[tt] or [REF].pdb[ref] file. By default, all frames all written to ",
@@ -266,7 +266,11 @@ int gmx_trjconv(int argc, char* argv[])
         "out the water from a trajectory of a protein in water.",
         "[BB]ALWAYS[bb] put the original trajectory on tape!",
         "We recommend to use the portable [REF].xtc[ref] format for your analysis",
-        "to save disk space and to have portable files.[PAR]",
+        "to save disk space and to have portable files. When writing [REF].tng[ref]",
+        "output the file will contain one molecule type of the correct count",
+        "if the selection name matches the molecule name and the selected atoms",
+        "match all atoms of that molecule. Otherwise the whole selection will",
+        "be treated as one single molecule containing all the selected atoms.[PAR]",
 
         "There are two options for fitting the trajectory to a reference",
         "either for essential dynamics analysis, etc.",
@@ -402,14 +406,14 @@ int gmx_trjconv(int argc, char* argv[])
     const char* fit[efNR + 1] = { nullptr,       "none",    "rot+trans",   "rotxy+transxy",
                                   "translation", "transxy", "progressive", nullptr };
 
-    static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
-    static gmx_bool bCenter = FALSE;
-    static int      skip_nr = 1, ndec = 3, nzero = 0;
-    static real     tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
-    static rvec     newbox = { 0, 0, 0 }, shift = { 0, 0, 0 }, trans = { 0, 0, 0 };
-    static char*    exec_command = nullptr;
-    static real     dropunder = 0, dropover = 0;
-    static gmx_bool bRound = FALSE;
+    gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
+    gmx_bool bCenter = FALSE;
+    int      skip_nr = 1, ndec = 3, nzero = 0;
+    real     tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
+    rvec     newbox = { 0, 0, 0 }, shift = { 0, 0, 0 }, trans = { 0, 0, 0 };
+    char*    exec_command = nullptr;
+    real     dropunder = 0, dropover = 0;
+    gmx_bool bRound = FALSE;
 
     t_pargs pa[] = {
         { "-skip", FALSE, etINT, { &skip_nr }, "Only write every nr-th frame" },
@@ -470,7 +474,7 @@ int gmx_trjconv(int argc, char* argv[])
           FALSE,
           etBOOL,
           { &bCONECT },
-          "Add conect records when writing [REF].pdb[ref] files. Useful "
+          "Add CONECT PDB records when writing [REF].pdb[ref] files. Useful "
           "for visualization of non-standard molecules, e.g. "
           "coarse grained ones" }
     };