/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014,2015, 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "config.h"
+#include "gmxpre.h"
#include <math.h>
#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/math/vec.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static const double bohr = 0.529177249; /* conversion factor to compensate for VMD plugin conversion... */
int gmx_spatial(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] calculates the spatial distribution function and ",
- "outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
- "For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated ",
- "in about 30 minutes, with most of the time dedicated to the two runs through ",
- "[TT]trjconv[tt] that are required to center everything properly. ",
- "This also takes a whole bunch of space (3 copies of the trajectory file). ",
- "Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
- "3-4 atoms in a widely mobile group (like a free amino acid in solution) works ",
- "well, or select the protein backbone in a stable folded structure to get the SDF ",
- "of solvent and look at the time-averaged solvation shell. ",
- "It is also possible using this program to generate the SDF based on some arbitrary ",
- "Cartesian coordinate. To do that, simply omit the preliminary [gmx-trjconv] steps. \n",
- "USAGE: \n",
- "1. Use [gmx-make_ndx] to create a group containing the atoms around which you want the SDF \n",
- "2. [TT]gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric -ur compact -pbc none[tt] \n",
- "3. [TT]gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans[tt] \n",
- "4. run [THISMODULE] on the [TT]c.tng[tt] output of step #3. \n",
- "5. Load [TT]grid.cube[tt] into VMD and view as an isosurface. \n",
- "[BB]Note[bb] that systems such as micelles will require [TT]gmx trjconv -pbc cluster[tt] between steps 1 and 2\n",
- "WARNINGS:[BR]",
- "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
- "However, the preparatory [TT]-fit rot+trans[tt] option to [gmx-trjconv] implies that your system will be rotating ",
- "and translating in space (in order that the selected group does not). Therefore the values that are ",
- "returned will only be valid for some region around your central group/coordinate that has full overlap ",
- "with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
- "It is up to the user to ensure that this is the case. \n",
- "BUGS:[BR]",
- "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
- "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins)",
- "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
- "with an increased [TT]-nab[tt] value. \n",
- "RISKY OPTIONS:[BR]",
- "To reduce the amount of space and time required, you can output only the coords ",
- "that are going to be used in the first and subsequent run through [gmx-trjconv]. ",
- "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
- "memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt] ",
- "option value. \n"
+ "[THISMODULE] calculates the spatial distribution function and",
+ "outputs it in a form that can be read by VMD as Gaussian98 cube format.",
+ "For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated",
+ "in about 30 minutes, with most of the time dedicated to the two runs through",
+ "[TT]trjconv[tt] that are required to center everything properly.",
+ "This also takes a whole bunch of space (3 copies of the trajectory file).",
+ "Still, the pictures are pretty and very informative when the fitted selection is properly made.",
+ "3-4 atoms in a widely mobile group (like a free amino acid in solution) works",
+ "well, or select the protein backbone in a stable folded structure to get the SDF",
+ "of solvent and look at the time-averaged solvation shell.",
+ "It is also possible using this program to generate the SDF based on some arbitrary",
+ "Cartesian coordinate. To do that, simply omit the preliminary [gmx-trjconv] steps.",
+ "",
+ "Usage:",
+ "",
+ "1. Use [gmx-make_ndx] to create a group containing the atoms around which you want the SDF",
+ "2. [TT]gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric -ur compact -pbc none[tt]",
+ "3. [TT]gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans[tt]",
+ "4. run [THISMODULE] on the [TT]c.tng[tt] output of step #3.",
+ "5. Load [TT]grid.cube[tt] into VMD and view as an isosurface.",
+ "",
+ "[BB]Note[bb] that systems such as micelles will require [TT]gmx trjconv -pbc cluster[tt] between steps 1 and 2.",
+ "",
+ "Warnings",
+ "^^^^^^^^",
+ "",
+ "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy.",
+ "However, the preparatory [TT]-fit rot+trans[tt] option to [gmx-trjconv] implies that your system will be rotating",
+ "and translating in space (in order that the selected group does not). Therefore the values that are",
+ "returned will only be valid for some region around your central group/coordinate that has full overlap",
+ "with system volume throughout the entire translated/rotated system over the course of the trajectory.",
+ "It is up to the user to ensure that this is the case.",
+ "",
+ "Risky options",
+ "^^^^^^^^^^^^^",
+ "",
+ "To reduce the amount of space and time required, you can output only the coords",
+ "that are going to be used in the first and subsequent run through [gmx-trjconv].",
+ "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since",
+ "memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt]",
+ "option value."
+ };
+ const char *bugs[] = {
+ "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected "
+ "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins) "
+ "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again "
+ "with an increased [TT]-nab[tt] value."
};
static gmx_bool bPBC = FALSE;
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff