<TR>
<TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=genbox.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>genbox</B></A> </TD>
+<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>solvate</B></A> </TD>
<TD><IMG SRC=../images/flow_vrule.gif></TD>
</TR>
velocities, you can also use a <a href="pdb.html">pdb</a> file in all programs.
To generate a box of solvent molecules
around the peptide, the program
-<a href="genbox.html">genbox</a> is used. First the program
+<a href="solvate.html">gmx solvate</a> is used. First the program
<a href="editconf.html">editconf</a> should be used to
define a box of appropriate size around the molecule.
-<a href="genbox.html">genbox</a>
-dissolves a solute molecule (the peptide) into any solvent (in this
-case water). The output of <TT><a href="genbox.html">genbox</a></TT> is a gromos structure file of
-the peptide dissolved in water. The <a href="genbox.html">genbox</a> program also changes the
+<a href="solvate.html">gmx solvate</a>
+solvates a solute molecule (the peptide) into any solvent (in this
+case water). The output of <TT><a href="solvate.html">gmx solvate</a></TT> is a gromos structure file of
+the peptide solvated in water. The <a href="solvate.html">gmx solvate</a> program also changes the
molecular topology file (generated by <a href="pdb2gmx.html">pdb2gmx</a>) to add solvent
to the topology.
<P></P>
"either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
- "For larger ions, e.g. sulfate we recommended using [gmx-genbox]."
+ "For larger ions, e.g. sulfate we recommended using [gmx-insert-molecules]."
};
const char *bugs[] = {
"If you specify a salt concentration existing ions are not taken into "
* 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 "genbox-addconf.h"
+#include "addconf.h"
#ifdef HAVE_CONFIG_H
#include <config.h>
fprintf(stderr, "Removed %d atoms that were outside the box\n", nremove);
}
- /* Define grid stuff for genbox */
+ /* Define grid stuff */
/* Largest VDW radius */
snew(r_all, natoms_prot+natoms_solvt);
for (i = j = 0; i < natoms_prot; i++, j++)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_GMXPREPROCESS_GENBOX_ADDCONF_H
-#define GMX_GMXPREPROCESS_GENBOX_ADDCONF_H
+#ifndef GMX_GMXPREPROCESS_ADDCONF_H
+#define GMX_GMXPREPROCESS_ADDCONF_H
#include "typedefs.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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 "insert-molecules.h"
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "smalloc.h"
+#include "string2.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/fileio/confio.h"
+#include "macros.h"
+#include "gromacs/random/random.h"
+#include "gromacs/fileio/futil.h"
+#include "atomprop.h"
+#include "names.h"
+#include "vec.h"
+#include "gmx_fatal.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "addconf.h"
+#include "read-conformation.h"
+#include "pbc.h"
+#include "xvgr.h"
+
+static gmx_bool in_box(t_pbc *pbc, rvec x)
+{
+ rvec box_center, dx;
+ int shift;
+
+ /* pbc_dx_aiuc only works correctly with the rectangular box center */
+ calc_box_center(ecenterRECT, pbc->box, box_center);
+
+ shift = pbc_dx_aiuc(pbc, x, box_center, dx);
+
+ return (shift == CENTRAL);
+}
+
+/* This is a (maybe) slow workaround to avoid the neighbor searching in addconf.c, which
+ * leaks memory (May 2012). The function could be deleted as soon as the memory leaks
+ * there are fixed.
+ * However, when inserting a small molecule in a system containing not too many atoms,
+ * allPairsDistOk is probably even faster than the other code.
+ */
+static gmx_bool
+allPairsDistOk(t_atoms *atoms, rvec *x, real *r,
+ int ePBC, matrix box,
+ t_atoms *atoms_insrt, rvec *x_n, real *r_insrt)
+{
+ int i, j;
+ rvec dx;
+ real n2, r2;
+ t_pbc pbc;
+
+ set_pbc(&pbc, ePBC, box);
+ for (i = 0; i < atoms->nr; i++)
+ {
+ for (j = 0; j < atoms_insrt->nr; j++)
+ {
+ pbc_dx(&pbc, x[i], x_n[j], dx);
+ n2 = norm2(dx);
+ r2 = sqr(r[i]+r_insrt[j]);
+ if (n2 < r2)
+ {
+ return FALSE;
+ }
+ }
+ }
+ return TRUE;
+}
+
+/* enum for random rotations of inserted solutes */
+enum {
+ en_rot, en_rotXYZ, en_rotZ, en_rotNone, en_NR
+};
+
+static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
+ t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
+ gmx_atomprop_t aps,
+ real r_distance, real r_scale, real rshell,
+ const output_env_t oenv,
+ const char* posfn, const rvec deltaR, int enum_rot,
+ gmx_bool bCheckAllPairDist)
+{
+ t_pbc pbc;
+ static char *title_insrt;
+ t_atoms atoms_insrt;
+ rvec *x_insrt, *x_n;
+ real *r_insrt;
+ int ePBC_insrt;
+ matrix box_insrt;
+ int i, mol, onr, ncol;
+ real alfa = 0., beta = 0., gamma = 0.;
+ rvec offset_x;
+ int trial;
+ double **rpos;
+ gmx_rng_t rng;
+
+ rng = gmx_rng_init(seed);
+ set_pbc(&pbc, ePBC, box);
+
+ /* read number of atoms of insert molecules */
+ get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
+ if (atoms_insrt.nr == 0)
+ {
+ gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
+ }
+ /* allocate memory for atom coordinates of insert molecules */
+ snew(x_insrt, atoms_insrt.nr);
+ snew(r_insrt, atoms_insrt.nr);
+ snew(atoms_insrt.resinfo, atoms_insrt.nr);
+ snew(atoms_insrt.atomname, atoms_insrt.nr);
+ snew(atoms_insrt.atom, atoms_insrt.nr);
+ atoms_insrt.pdbinfo = NULL;
+ snew(x_n, atoms_insrt.nr);
+ snew(title_insrt, STRLEN);
+
+ /* read residue number, residue names, atomnames, coordinates etc. */
+ fprintf(stderr, "Reading molecule configuration \n");
+ read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
+ &ePBC_insrt, box_insrt);
+ fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
+ title_insrt, atoms_insrt.nr, atoms_insrt.nres);
+ srenew(atoms_insrt.resinfo, atoms_insrt.nres);
+
+ /* initialise van der waals arrays for inserted molecules */
+ mk_vdw(&atoms_insrt, r_insrt, aps, r_distance, r_scale);
+
+ /* With -ip, take nmol_insrt from file posfn */
+ if (posfn != NULL)
+ {
+ nmol_insrt = read_xvg(posfn, &rpos, &ncol);
+ if (ncol != 3)
+ {
+ gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
+ }
+ fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
+ }
+
+ srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
+ srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
+ srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
+ srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
+ srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
+
+ trial = mol = 0;
+ while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
+ {
+ fprintf(stderr, "\rTry %d", trial++);
+ for (i = 0; (i < atoms_insrt.nr); i++)
+ {
+ copy_rvec(x_insrt[i], x_n[i]);
+ }
+ switch (enum_rot)
+ {
+ case en_rotXYZ:
+ alfa = 2*M_PI * gmx_rng_uniform_real(rng);
+ beta = 2*M_PI * gmx_rng_uniform_real(rng);
+ gamma = 2*M_PI * gmx_rng_uniform_real(rng);
+ break;
+ case en_rotZ:
+ alfa = beta = 0.;
+ gamma = 2*M_PI * gmx_rng_uniform_real(rng);
+ break;
+ case en_rotNone:
+ alfa = beta = gamma = 0.;
+ break;
+ }
+ if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
+ {
+ rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
+ }
+ if (posfn == NULL)
+ {
+ /* insert at random positions */
+ offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
+ offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
+ offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
+ make_new_box(atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
+ if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
+ {
+ continue;
+ }
+ }
+ else
+ {
+ /* Insert at positions taken from option -ip file */
+ offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
+ offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
+ offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
+ for (i = 0; i < atoms_insrt.nr; i++)
+ {
+ rvec_inc(x_n[i], offset_x);
+ }
+ }
+
+ onr = atoms->nr;
+
+ /* This is a (maybe) slow workaround to avoid too many calls of add_conf, which
+ * leaks memory (status May 2012). If the momory leaks in add_conf() are fixed,
+ * this check could be removed. Note, however, that allPairsDistOk is probably
+ * even faster than add_conf() when inserting a small molecule into a moderately
+ * small system.
+ */
+ if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *r, ePBC, box, &atoms_insrt, x_n, r_insrt))
+ {
+ continue;
+ }
+
+ add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
+ &atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
+
+ if (atoms->nr == (atoms_insrt.nr+onr))
+ {
+ mol++;
+ fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
+ }
+ }
+ gmx_rng_destroy(rng);
+ srenew(atoms->resinfo, atoms->nres);
+ srenew(atoms->atomname, atoms->nr);
+ srenew(atoms->atom, atoms->nr);
+ srenew(*x, atoms->nr);
+ srenew(*r, atoms->nr);
+
+ fprintf(stderr, "\n");
+ /* print number of molecules added */
+ fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
+ mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
+
+ return title_insrt;
+}
+
+int gmx_insert_molecules(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "[THISMODULE] inserts [TT]-nmol[tt] copies of the system specified in",
+ "the [TT]-ci[tt] input file. The insertions take place either into",
+ "vacant space in the solute conformation given with [TT]-f[tt], or",
+ "into an empty box given by [TT]-box[tt]. Specifying both [TT]-f[tt]",
+ "and [TT]-box[tt] behaves like [TT]-f[tt], but places a new box",
+ "around the solute before insertions. Any velocities present are",
+ "discarded.[PAR]",
+
+ "By default, the insertion positions are random (with initial seed",
+ "specified by [TT]-seed[tt]). The program iterates until [TT]-nmol[tt]",
+ "molecules have been inserted in the box. Molecules are not inserted",
+ "where the distance between any existing atom and any atom of ",
+ "the inserted molecule is less than the sum of the van der Waals radii of ",
+ "both atoms. A database ([TT]vdwradii.dat[tt]) of van der Waals radii is ",
+ "read by the program, and atoms not in the database are ",
+ "assigned a default distance [TT]-vdwd[tt].[PAR]",
+
+ "A total of [TT]-nmol[tt] * [TT]-try[tt] insertion attempts are made",
+ "before giving up. Increase [TT]-try[tt] if you have several small",
+ "holes to fill. Option [TT]-rot[tt] specifies whether the insertion",
+ "molecules are randomly oriented before insertion attempts.[PAR]",
+
+ "Alternatively, the molecules can be inserted only at positions defined in",
+ "positions.dat ([TT]-ip[tt]). That file should have 3 columns (x,y,z),",
+ "that give the displacements compared to the input molecule position",
+ "([TT]-ci[tt]). Hence, if that file should contain the absolute",
+ "positions, the molecule must be centered on (0,0,0) before using",
+ "[THISMODULE] (e.g. from [gmx-editconf] [TT]-center[tt]).",
+ "Comments in that file starting with # are ignored. Option [TT]-dr[tt]",
+ "defines the maximally allowed displacements during insertial trials.",
+ "[TT]-try[tt] and [TT]-rot[tt] work as in the default mode (see above).",
+ "[PAR]",
+ };
+
+ const char *bugs[] = {
+ "Molecules must be whole in the initial configurations.",
+ "Many repeated neighbor searchings with -ci blows up the allocated memory. "
+ "Option -allpair avoids this using all-to-all distance checks (slow for large systems)"
+ };
+
+ /* parameter data */
+ gmx_bool bProt, bBox;
+ const char *conf_prot, *confout;
+ real *r;
+ char *title_ins = NULL;
+ gmx_atomprop_t aps;
+
+ /* protein configuration data */
+ char *title = NULL;
+ t_atoms atoms;
+ rvec *x = NULL;
+ int ePBC = -1;
+ matrix box;
+
+ t_filenm fnm[] = {
+ { efSTX, "-f", "protein", ffOPTRD },
+ { efSTX, "-ci", "insert", ffREAD},
+ { efDAT, "-ip", "positions", ffOPTRD},
+ { efSTO, NULL, NULL, ffWRITE},
+ };
+#define NFILE asize(fnm)
+
+ static int nmol_ins = 0, nmol_try = 10, seed = 1997, enum_rot;
+ static real r_distance = 0.105, r_scale = 0.57;
+ static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
+ static gmx_bool bCheckAllPairDist = FALSE;
+ output_env_t oenv;
+ const char *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
+ t_pargs pa[] = {
+ { "-box", FALSE, etRVEC, {new_box},
+ "Box size (in nm)" },
+ { "-nmol", FALSE, etINT, {&nmol_ins},
+ "Number of extra molecules to insert" },
+ { "-try", FALSE, etINT, {&nmol_try},
+ "Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
+ { "-seed", FALSE, etINT, {&seed},
+ "Random generator seed"},
+ { "-vdwd", FALSE, etREAL, {&r_distance},
+ "Default van der Waals distance"},
+ { "-vdwscale", FALSE, etREAL, {&r_scale},
+ "HIDDENScale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
+ { "-dr", FALSE, etRVEC, {deltaR},
+ "Allowed displacement in x/y/z from positions in [TT]-ip[tt] file" },
+ { "-rot", FALSE, etENUM, {enum_rot_string},
+ "rotate inserted molecules randomly" },
+ { "-allpair", FALSE, etBOOL, {&bCheckAllPairDist},
+ "Avoid momory leaks during neighbor searching with option -ci. May be slow for large systems." },
+ };
+
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
+
+ bProt = opt2bSet("-f", NFILE, fnm);
+ bBox = opt2parg_bSet("-box", asize(pa), pa);
+ enum_rot = nenum(enum_rot_string);
+
+ /* check input */
+ const char *insertionMoleculeFileName = opt2fn("-ci", NFILE, fnm);
+ if (!gmx_fexist(insertionMoleculeFileName))
+ {
+ gmx_fatal(FARGS,
+ "A molecule conformation to insert is required in -ci. %s was not found!",
+ insertionMoleculeFileName);
+ }
+ if (nmol_ins <= 0 && !opt2bSet("-ip", NFILE, fnm))
+ {
+ gmx_fatal(FARGS, "Either -nmol must be larger than 0, "
+ "or positions must be given with -ip");
+ }
+ if (!bProt && !bBox)
+ {
+ gmx_fatal(FARGS, "When no solute (-f) is specified, "
+ "a box size (-box) must be specified");
+ }
+
+ aps = gmx_atomprop_init();
+
+ if (bProt)
+ {
+ /*generate a solute configuration */
+ conf_prot = opt2fn("-f", NFILE, fnm);
+ title = read_conformation(conf_prot, &atoms, &x, NULL, &r, &ePBC, box,
+ aps, r_distance, r_scale);
+ if (atoms.nr == 0)
+ {
+ fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
+ bProt = FALSE;
+ }
+ }
+ else
+ {
+ atoms.nr = 0;
+ atoms.nres = 0;
+ atoms.resinfo = NULL;
+ atoms.atomname = NULL;
+ atoms.atom = NULL;
+ atoms.pdbinfo = NULL;
+ x = NULL;
+ r = NULL;
+ }
+ if (bBox)
+ {
+ ePBC = epbcXYZ;
+ clear_mat(box);
+ box[XX][XX] = new_box[XX];
+ box[YY][YY] = new_box[YY];
+ box[ZZ][ZZ] = new_box[ZZ];
+ }
+ if (det(box) == 0)
+ {
+ gmx_fatal(FARGS, "Undefined solute box.\nCreate one with gmx editconf "
+ "or give explicit -box command line option");
+ }
+
+ /* add nmol_ins molecules of atoms_ins
+ in random orientation at random place */
+ title_ins = insert_mols(insertionMoleculeFileName, nmol_ins, nmol_try, seed,
+ &atoms, &x, &r, ePBC, box, aps,
+ r_distance, r_scale, 0,
+ oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
+ bCheckAllPairDist);
+
+ /* write new configuration to file confout */
+ confout = ftp2fn(efSTO, NFILE, fnm);
+ fprintf(stderr, "Writing generated configuration to %s\n", confout);
+ if (bProt)
+ {
+ write_sto_conf(confout, title, &atoms, x, NULL, ePBC, box);
+ /* print box sizes and box type to stderr */
+ fprintf(stderr, "%s\n", title);
+ }
+ else
+ {
+ write_sto_conf(confout, title_ins, &atoms, x, NULL, ePBC, box);
+ }
+
+ /* print size of generated configuration */
+ fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
+ atoms.nr, atoms.nres);
+
+ gmx_atomprop_destroy(aps);
+
+ return 0;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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.
+ */
+#ifndef GMX_GMXPREPROCESS_INSERT_MOLECULES_H
+#define GMX_GMXPREPROCESS_INSERT_MOLECULES_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
+
+int gmx_insert_molecules(int argc, char *argv[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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 "read-conformation.h"
+
+#include "gromacs/fileio/confio.h"
+#include "atomprop.h"
+#include "types/simple.h"
+#include "types/atoms.h"
+#include "smalloc.h"
+
+void mk_vdw(t_atoms *a, real rvdw[], gmx_atomprop_t aps,
+ real r_distance, real r_scale)
+{
+ int i;
+
+ /* initialise van der waals arrays of configuration */
+ fprintf(stderr, "Initialising van der waals distances...\n");
+ for (i = 0; (i < a->nr); i++)
+ {
+ if (!gmx_atomprop_query(aps, epropVDW,
+ *(a->resinfo[a->atom[i].resind].name),
+ *(a->atomname[i]), &(rvdw[i])))
+ {
+ rvdw[i] = r_distance;
+ }
+ else
+ {
+ rvdw[i] *= r_scale;
+ }
+ }
+}
+
+char *read_conformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
+ real **r, int *ePBC, matrix box, gmx_atomprop_t aps,
+ real r_distance, real r_scale)
+{
+ char *title;
+ int natoms;
+
+ snew(title, STRLEN);
+ get_stx_coordnum(confin, &natoms);
+
+ /* allocate memory for atom coordinates of configuration */
+ snew(*x, natoms);
+ if (v)
+ {
+ snew(*v, natoms);
+ }
+ snew(*r, natoms);
+ init_t_atoms(atoms, natoms, FALSE);
+
+ /* read residue number, residue names, atomnames, coordinates etc. */
+ fprintf(stderr, "Reading solute configuration%s\n", v ? " and velocities" : "");
+ read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
+ fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
+ title, atoms->nr, atoms->nres);
+
+ mk_vdw(atoms, *r, aps, r_distance, r_scale);
+
+ return title;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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.
+ */
+#ifndef GMX_GMXPREPROCESS_READ_CONFORMATION_H
+#define GMX_GMXPREPROCESS_READ_CONFORMATION_H
+
+#include "types/simple.h"
+#include "types/atoms.h"
+#include "atomprop.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! Helper function reading VDW radii
+ *
+ * Used directly and indirectly by generate-velocities and
+ * insert-molecules. */
+void mk_vdw(t_atoms *a, real rvdw[], gmx_atomprop_t aps,
+ real r_distance, real r_scale);
+
+/*! Helper function to read a conformation from a file.
+ *
+ * Used by generate-velocities and insert-molecules. */
+char *read_conformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
+ real **r, int *ePBC, matrix box, gmx_atomprop_t aps,
+ real r_distance, real r_scale);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
* 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 "genbox.h"
+#include "solvate.h"
#ifdef HAVE_CONFIG_H
#include <config.h>
#include "typedefs.h"
#include "smalloc.h"
#include "string2.h"
-#include "physics.h"
#include "gromacs/fileio/confio.h"
-#include "txtdump.h"
-#include <math.h>
#include "macros.h"
-#include "gromacs/random/random.h"
#include "gromacs/fileio/futil.h"
#include "atomprop.h"
#include "names.h"
#include "vec.h"
#include "gmx_fatal.h"
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
#include "gromacs/gmxlib/conformation-utilities.h"
-#include "genbox-addconf.h"
+#include "addconf.h"
+#include "read-conformation.h"
#include "gromacs/fileio/pdbio.h"
#include "pbc.h"
-#include "xvgr.h"
#ifdef DEBUG
static void print_stat(rvec *x, int natoms, matrix box)
}
#endif
-static gmx_bool in_box(t_pbc *pbc, rvec x)
-{
- rvec box_center, dx;
- int shift;
-
- /* pbc_dx_aiuc only works correctly with the rectangular box center */
- calc_box_center(ecenterRECT, pbc->box, box_center);
-
- shift = pbc_dx_aiuc(pbc, x, box_center, dx);
-
- return (shift == CENTRAL);
-}
-
-static void mk_vdw(t_atoms *a, real rvdw[], gmx_atomprop_t aps,
- real r_distance, real r_scale)
-{
- int i;
-
- /* initialise van der waals arrays of configuration */
- fprintf(stderr, "Initialising van der waals distances...\n");
- for (i = 0; (i < a->nr); i++)
- {
- if (!gmx_atomprop_query(aps, epropVDW,
- *(a->resinfo[a->atom[i].resind].name),
- *(a->atomname[i]), &(rvdw[i])))
- {
- rvdw[i] = r_distance;
- }
- else
- {
- rvdw[i] *= r_scale;
- }
- }
-}
-
typedef struct {
char *name;
int natoms;
}
}
-/* This is a (maybe) slow workaround to avoid the neighbor searching in genbox_addconf.c, which
- * leaks memory (May 2012). The function could be deleted as soon as the memory leaks
- * there are fixed.
- * However, when inserting a small molecule in a system containing not too many atoms,
- * allPairsDistOk is probably even faster than the other code.
- */
-static gmx_bool
-allPairsDistOk(t_atoms *atoms, rvec *x, real *r,
- int ePBC, matrix box,
- t_atoms *atoms_insrt, rvec *x_n, real *r_insrt)
-{
- int i, j;
- rvec dx;
- real n2, r2;
- t_pbc pbc;
-
- set_pbc(&pbc, ePBC, box);
- for (i = 0; i < atoms->nr; i++)
- {
- for (j = 0; j < atoms_insrt->nr; j++)
- {
- pbc_dx(&pbc, x[i], x_n[j], dx);
- n2 = norm2(dx);
- r2 = sqr(r[i]+r_insrt[j]);
- if (n2 < r2)
- {
- return FALSE;
- }
- }
- }
- return TRUE;
-}
-
-/* enum for random rotations of inserted solutes */
-enum {
- en_rot, en_rotXYZ, en_rotZ, en_rotNone, en_NR
-};
-
-static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
- t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
- gmx_atomprop_t aps,
- real r_distance, real r_scale, real rshell,
- const output_env_t oenv,
- const char* posfn, const rvec deltaR, int enum_rot,
- gmx_bool bCheckAllPairDist)
-{
- t_pbc pbc;
- static char *title_insrt;
- t_atoms atoms_insrt;
- rvec *x_insrt, *x_n;
- real *r_insrt;
- int ePBC_insrt;
- matrix box_insrt;
- int i, mol, onr, ncol;
- real alfa = 0., beta = 0., gamma = 0.;
- rvec offset_x;
- int trial;
- double **rpos;
- gmx_rng_t rng;
-
- rng = gmx_rng_init(seed);
- set_pbc(&pbc, ePBC, box);
-
- /* read number of atoms of insert molecules */
- get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
- if (atoms_insrt.nr == 0)
- {
- gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
- }
- /* allocate memory for atom coordinates of insert molecules */
- snew(x_insrt, atoms_insrt.nr);
- snew(r_insrt, atoms_insrt.nr);
- snew(atoms_insrt.resinfo, atoms_insrt.nr);
- snew(atoms_insrt.atomname, atoms_insrt.nr);
- snew(atoms_insrt.atom, atoms_insrt.nr);
- atoms_insrt.pdbinfo = NULL;
- snew(x_n, atoms_insrt.nr);
- snew(title_insrt, STRLEN);
-
- /* read residue number, residue names, atomnames, coordinates etc. */
- fprintf(stderr, "Reading molecule configuration \n");
- read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
- &ePBC_insrt, box_insrt);
- fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
- title_insrt, atoms_insrt.nr, atoms_insrt.nres);
- srenew(atoms_insrt.resinfo, atoms_insrt.nres);
-
- /* initialise van der waals arrays of insert molecules */
- mk_vdw(&atoms_insrt, r_insrt, aps, r_distance, r_scale);
-
- /* With -ip, take nmol_insrt from file posfn */
- if (posfn != NULL)
- {
- nmol_insrt = read_xvg(posfn, &rpos, &ncol);
- if (ncol != 3)
- {
- gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
- }
- fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
- }
-
- srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
- srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
-
- trial = mol = 0;
- while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
- {
- fprintf(stderr, "\rTry %d", trial++);
- for (i = 0; (i < atoms_insrt.nr); i++)
- {
- copy_rvec(x_insrt[i], x_n[i]);
- }
- switch (enum_rot)
- {
- case en_rotXYZ:
- alfa = 2*M_PI * gmx_rng_uniform_real(rng);
- beta = 2*M_PI * gmx_rng_uniform_real(rng);
- gamma = 2*M_PI * gmx_rng_uniform_real(rng);
- break;
- case en_rotZ:
- alfa = beta = 0.;
- gamma = 2*M_PI * gmx_rng_uniform_real(rng);
- break;
- case en_rotNone:
- alfa = beta = gamma = 0.;
- break;
- }
- if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
- {
- rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
- }
- if (posfn == NULL)
- {
- /* insert at random positions */
- offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
- offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
- offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
- make_new_box(atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
- if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
- {
- continue;
- }
- }
- else
- {
- /* Insert at positions taken from option -ip file */
- offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
- offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
- offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
- for (i = 0; i < atoms_insrt.nr; i++)
- {
- rvec_inc(x_n[i], offset_x);
- }
- }
-
- onr = atoms->nr;
-
- /* This is a (maybe) slow workaround to avoid too many calls of add_conf, which
- * leaks memory (status May 2012). If the momory leaks in add_conf() are fixed,
- * this check could be removed. Note, however, that allPairsDistOk is probably
- * even faster than add_conf() when inserting a small molecule into a moderately
- * small system.
- */
- if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *r, ePBC, box, &atoms_insrt, x_n, r_insrt))
- {
- continue;
- }
-
- add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
- &atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
-
- if (atoms->nr == (atoms_insrt.nr+onr))
- {
- mol++;
- fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
- }
- }
- gmx_rng_destroy(rng);
- srenew(atoms->resinfo, atoms->nres);
- srenew(atoms->atomname, atoms->nr);
- srenew(atoms->atom, atoms->nr);
- srenew(*x, atoms->nr);
- srenew(*r, atoms->nr);
-
- fprintf(stderr, "\n");
- /* print number of molecules added */
- fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
- mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
-
- return title_insrt;
-}
-
/* Make a new configuration by adding boxes*/
static void make_new_conformation(t_atoms *atoms, rvec *x, rvec *v, real *r, matrix box, ivec n_box)
{
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
- /* initialise van der waals arrays of solvent configuration */
+ /* initialise van der waals arrays for solvent configuration */
mk_vdw(atoms_solvt, r_solvt, aps, r_distance, r_scale);
/* calculate the box multiplication factors n_box[0...DIM] */
*atoms_added, *residues_added);
}
-static char *read_prot(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
- real **r, int *ePBC, matrix box, gmx_atomprop_t aps,
- real r_distance, real r_scale)
-{
- char *title;
- int natoms;
-
- snew(title, STRLEN);
- get_stx_coordnum(confin, &natoms);
-
- /* allocate memory for atom coordinates of configuration 1 */
- snew(*x, natoms);
- if (v)
- {
- snew(*v, natoms);
- }
- snew(*r, natoms);
- init_t_atoms(atoms, natoms, FALSE);
-
- /* read residue number, residue names, atomnames, coordinates etc. */
- fprintf(stderr, "Reading solute configuration%s\n", v ? " and velocities" : "");
- read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
- fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
- title, atoms->nr, atoms->nres);
-
- /* initialise van der waals arrays of configuration 1 */
- mk_vdw(atoms, *r, aps, r_distance, r_scale);
-
- return title;
-}
-
static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
gmx_atomprop_t aps)
{
#undef TEMP_FILENM
}
-int gmx_genbox(int argc, char *argv[])
+int gmx_solvate(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] can do one of 4 things:[PAR]",
+ "[THISMODULE] can do one of 2 things:[PAR]",
- "1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt]. Or specify [TT]-cs[tt] and",
- "[TT]-cp[tt] with a structure file with a box, but without atoms.[PAR]",
+ "1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt].",
+ "Or specify [TT]-cs[tt] and [TT]-cp[tt] with a structure file with",
+ "a box, but without atoms.[PAR]",
"2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
"molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
"The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
"unless [TT]-box[tt] is set.",
"If you want the solute to be centered in the box,",
- "the program [TT]editconf[tt] has sophisticated options",
+ "the program [gmx-editconf] has sophisticated options",
"to change the box dimensions and center the solute.",
"Solvent molecules are removed from the box where the ",
"distance between any atom of the solute molecule(s) and any atom of ",
"solvent molecules if they contain atoms that are not in the database.",
"[PAR]",
- "3) Insert a number ([TT]-nmol[tt]) of extra molecules ([TT]-ci[tt]) ",
- "at random positions.",
- "The program iterates until [TT]nmol[tt] molecules",
- "have been inserted in the box. To test whether an insertion is ",
- "successful the same van der Waals criterium is used as for removal of ",
- "solvent molecules. When no appropriately-sized ",
- "holes (holes that can hold an extra molecule) are available, the ",
- "program tries for [TT]-nmol[tt] * [TT]-try[tt] times before giving up. ",
- "Increase [TT]-try[tt] if you have several small holes to fill.",
- "Option [TT]-rot[tt] defines if the molecules are randomly oriented.",
- "[PAR]",
-
- "4) Insert a number of molecules ([TT]-ci[tt]) at positions defined in",
- "positions.dat ([TT]-ip[tt]). positions.dat should have 3 columns (x/y/z),",
- "that give the displacements compared to the input molecule position ([TT]-ci[tt]).",
- "Hence, if positions.dat should contain the absolut positions, the molecule ",
- "must be centered to 0/0/0 before using genbox (use, e.g., editconf -center).",
- "Comments in positions.dat starting with # are ignored. Option [TT]-dr[tt]",
- "defines the maximally allowed displacements during insertial trials.",
- "[TT]-try[tt] and [TT]-rot[tt] work as in mode (3) (see above)",
- "[PAR]",
-
- "If you need to do more than one of the above operations, it can be",
- "best to call [THISMODULE] separately for each operation, so that",
- "you are sure of the order in which the operations occur.[PAR]",
-
"The default solvent is Simple Point Charge water (SPC), with coordinates ",
"from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
"for other 3-site water models, since a short equibilibration will remove",
const char *bugs[] = {
"Molecules must be whole in the initial configurations.",
- "Many repeated neighbor searchings with -ci blows up the allocated memory. "
- "Option -allpair avoids this using all-to-all distance checks (slow for large systems)"
};
/* parameter data */
- gmx_bool bSol, bProt, bBox;
+ gmx_bool bProt, bBox;
const char *conf_prot, *confout;
- int bInsert;
real *r;
- char *title_ins;
gmx_atomprop_t aps;
/* protein configuration data */
t_filenm fnm[] = {
{ efSTX, "-cp", "protein", ffOPTRD },
- { efSTX, "-cs", "spc216", ffLIBOPTRD},
- { efSTX, "-ci", "insert", ffOPTRD},
- { efDAT, "-ip", "positions", ffOPTRD},
+ { efSTX, "-cs", "spc216", ffLIBRD},
{ efSTO, NULL, NULL, ffWRITE},
{ efTOP, NULL, NULL, ffOPTRW},
};
#define NFILE asize(fnm)
- static int nmol_ins = 0, nmol_try = 10, seed = 1997, enum_rot;
static real r_distance = 0.105, r_shell = 0, r_scale = 0.57;
- static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
- static gmx_bool bReadV = FALSE, bCheckAllPairDist = FALSE;
+ static rvec new_box = {0.0, 0.0, 0.0};
+ static gmx_bool bReadV = FALSE;
static int max_sol = 0;
output_env_t oenv;
- const char *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
"Box size (in nm)" },
- { "-nmol", FALSE, etINT, {&nmol_ins},
- "Number of extra molecules to insert" },
- { "-try", FALSE, etINT, {&nmol_try},
- "Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
- { "-seed", FALSE, etINT, {&seed},
- "Random generator seed"},
{ "-vdwd", FALSE, etREAL, {&r_distance},
"Default van der Waals distance"},
{ "-vdwscale", FALSE, etREAL, {&r_scale},
"Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
{ "-vel", FALSE, etBOOL, {&bReadV},
"Keep velocities from input solute and solvent" },
- { "-dr", FALSE, etRVEC, {deltaR},
- "Allowed displacement in x/y/z from positions in [TT]-ip[tt] file" },
- { "-rot", FALSE, etENUM, {enum_rot_string},
- "rotate inserted molecules randomly" },
- { "-allpair", FALSE, etBOOL, {&bCheckAllPairDist},
- "Avoid momory leaks during neighbor searching with option -ci. May be slow for large systems." },
};
if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
return 0;
}
- bInsert = opt2bSet("-ci", NFILE, fnm) && ((nmol_ins > 0) || opt2bSet("-ip", NFILE, fnm));
- bSol = opt2bSet("-cs", NFILE, fnm);
+ const char *solventFileName = opt2fn("-cs", NFILE, fnm);
bProt = opt2bSet("-cp", NFILE, fnm);
bBox = opt2parg_bSet("-box", asize(pa), pa);
- enum_rot = nenum(enum_rot_string);
/* check input */
- if (bInsert && (nmol_ins <= 0 && !opt2bSet("-ip", NFILE, fnm)))
- {
- gmx_fatal(FARGS, "When specifying inserted molecules (-ci), "
- "-nmol must be larger than 0 or positions must be given with -ip");
- }
if (!bProt && !bBox)
{
gmx_fatal(FARGS, "When no solute (-cp) is specified, "
if (bProt)
{
- /*generate a solute configuration */
+ /* Generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
- title = read_prot(conf_prot, &atoms, &x, bReadV ? &v : NULL, &r, &ePBC, box,
- aps, r_distance, r_scale);
+ title = read_conformation(conf_prot, &atoms, &x, bReadV ? &v : NULL, &r, &ePBC, box,
+ aps, r_distance, r_scale);
if (bReadV && !v)
{
fprintf(stderr, "Note: no velocities found\n");
bProt = FALSE;
}
}
- if (!bProt)
+ else
{
atoms.nr = 0;
atoms.nres = 0;
}
if (det(box) == 0)
{
- gmx_fatal(FARGS, "Undefined solute box.\nCreate one with editconf "
+ gmx_fatal(FARGS, "Undefined solute box.\nCreate one with gmx editconf "
"or give explicit -box command line option");
}
- /* add nmol_ins molecules of atoms_ins
- in random orientation at random place */
- if (bInsert)
- {
- title_ins = insert_mols(opt2fn("-ci", NFILE, fnm), nmol_ins, nmol_try, seed,
- &atoms, &x, &r, ePBC, box, aps,
- r_distance, r_scale, r_shell,
- oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
- bCheckAllPairDist);
- }
- else
- {
- title_ins = strdup("Generated by genbox");
- }
-
- /* add solvent */
- if (bSol)
- {
- add_solv(opt2fn("-cs", NFILE, fnm), &atoms, &x, v ? &v : NULL, &r, ePBC, box,
- aps, r_distance, r_scale, &atoms_added, &residues_added, r_shell, max_sol,
- oenv);
- }
+ add_solv(solventFileName, &atoms, &x, v ? &v : NULL, &r, ePBC, box,
+ aps, r_distance, r_scale, &atoms_added, &residues_added, r_shell, max_sol,
+ oenv);
/* write new configuration 1 to file confout */
confout = ftp2fn(efSTO, NFILE, fnm);
}
else
{
- write_sto_conf(confout, title_ins, &atoms, x, v, ePBC, box);
+ write_sto_conf(confout, "Generated by gmx solvate", &atoms, x, v, ePBC, box);
}
- sfree(title_ins);
-
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
atoms.nr, atoms.nres);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_GMXPREPROCESS_GENBOX_H
-#define GMX_GMXPREPROCESS_GENBOX_H
+#ifndef GMX_GMXPREPROCESS_SOLVATE_H
+#define GMX_GMXPREPROCESS_SOLVATE_H
#ifdef __cplusplus
extern "C" {
}
#endif
-int gmx_genbox(int argc, char *argv[]);
+int gmx_solvate(int argc, char *argv[]);
#ifdef __cplusplus
}
${testname}
${exename}
# files with code for test fixtures
- genbox.cpp
+ solvate.cpp
+ insert-molecules.cpp
)
gmx_register_integration_test(
${testname}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for insertion of molecules.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ */
+
+#include "../insert-molecules.h"
+#include "testutils/integrationtests.h"
+#include "testutils/cmdlinetest.h"
+#include "gromacs/fileio/futil.h"
+
+namespace
+{
+
+//! Helper typedef
+typedef int (*CMainFunction)(int argc, char *argv[]);
+
+//! Test fixture for insert-molecules
+class InsertMoleculesTest : public gmx::test::IntegrationTestFixture
+{
+ public:
+ //! Constructor
+ InsertMoleculesTest()
+ : ciFileName(fileManager_.getInputFilePath("x.gro")),
+ outputFileName(fileManager_.getTemporaryFilePath("out.gro")),
+ theFunction(gmx_insert_molecules)
+ {
+ caller.append("insert-molecules");
+ caller.addOption("-o", outputFileName);
+ }
+
+ public:
+ //! Name of file to use for -ci
+ std::string ciFileName;
+ //! Name of output file to use for -o
+ std::string outputFileName;
+ //! Helper object for managing the call to gmx_insert_molecules
+ gmx::test::CommandLine caller;
+ //! Points to the function to be tested
+ CMainFunction theFunction;
+};
+
+TEST_F(InsertMoleculesTest, f_ci_Works)
+{
+ caller.addOption("-f", fileManager_.getInputFilePath("spc-and-methanol.gro"));
+ caller.addOption("-nmol", "1");
+ caller.addOption("-ci", ciFileName);
+
+ ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+}
+
+TEST_F(InsertMoleculesTest, box_ci_Works)
+{
+ caller.addOption("-box", "4");
+ caller.addOption("-nmol", "5");
+ caller.addOption("-ci", ciFileName);
+
+ ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+}
+
+TEST_F(InsertMoleculesTest, f_box_ci_Works)
+{
+ caller.addOption("-f", fileManager_.getInputFilePath("spc-and-methanol.gro"));
+ caller.addOption("-box", "4");
+ caller.addOption("-nmol", "2");
+ caller.addOption("-ci", ciFileName);
+
+ ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+}
+
+// TODO Someone who knows what -ip is good for should write something
+// to test it
+
+} // namespace
*/
/*! \internal \file
* \brief
- * Tests for gmx traj
+ * Tests for solvation.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
*/
-#include "../genbox.h"
+#include "../solvate.h"
#include "testutils/integrationtests.h"
#include "testutils/cmdlinetest.h"
#include "gromacs/fileio/futil.h"
namespace
{
-//! Test fixture for genbox
-class Genbox : public gmx::test::IntegrationTestFixture
+//! Helper typedef
+typedef int (*CMainFunction)(int argc, char *argv[]);
+
+//! Test fixture for gmx solvate
+class SolvateTest : public gmx::test::IntegrationTestFixture
{
public:
//! Constructor
- Genbox()
+ SolvateTest()
: cpFileName(fileManager_.getInputFilePath("spc-and-methanol.gro")),
- ciFileName(fileManager_.getInputFilePath("x.gro")),
topFileName(fileManager_.getInputFilePath("spc-and-methanol.top")),
- outputFileName(fileManager_.getTemporaryFilePath("out.gro"))
+ outputFileName(fileManager_.getTemporaryFilePath("out.gro")),
+ theFunction(gmx_solvate)
{
- caller.append("genbox");
+ caller.append("solvate");
caller.addOption("-o", outputFileName);
}
public:
//! Name of file to use for -cp
std::string cpFileName;
- //! Name of file to use for -ci
- std::string ciFileName;
//! Name of input file to use for -p (if used)
std::string topFileName;
//! Name of output file to use for -o
std::string outputFileName;
- //! Helper object for managing the call to gmx_genbox
+ //! Helper object for managing the call to gmx_solvate
gmx::test::CommandLine caller;
+ //! Points to the function to be tested
+ CMainFunction theFunction;
};
-TEST_F(Genbox, cs_box_Works)
+TEST_F(SolvateTest, cs_box_Works)
{
caller.append("-cs"); // use default solvent box
caller.addOption("-box", "1.1");
- ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+ ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
}
-TEST_F(Genbox, cs_cp_Works)
+TEST_F(SolvateTest, cs_cp_Works)
{
caller.append("-cs"); // use default solvent box
caller.addOption("-cp", cpFileName);
- ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+ ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
}
-TEST_F(Genbox, cs_cp_p_Works)
+TEST_F(SolvateTest, cs_cp_p_Works)
{
caller.append("-cs"); // use default solvent box
caller.addOption("-cp", cpFileName);
gmx_file_copy(topFileName.c_str(), modifiableTopFileName.c_str(), true);
caller.addOption("-p", modifiableTopFileName);
- ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
-}
-
-TEST_F(Genbox, ci_Works)
-{
- caller.addOption("-cp", fileManager_.getInputFilePath("spc216.gro"));
- caller.addOption("-nmol", "2");
- caller.addOption("-ci", ciFileName);
- caller.addOption("-vdwd", "0.01"); // Make sure insertions happen
-
- ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+ ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
}
-// TODO Someone who knows what -ip is good for should write something
-// to test it
-
} // namespace
+++ /dev/null
-216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
- 648
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- 1.86206 1.86206 1.86206
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxpreprocess/grompp.h"
-#include "gromacs/gmxpreprocess/genbox.h"
+#include "gromacs/gmxpreprocess/solvate.h"
+#include "gromacs/gmxpreprocess/insert-molecules.h"
#include "gromacs/gmxpreprocess/pdb2gmx.h"
#include "gromacs/gmxpreprocess/protonate.h"
#include "gromacs/gmxpreprocess/x2top.h"
"Convert and manipulates structure files");
registerModule(manager, &gmx_eneconv, "eneconv",
"Convert energy files");
- registerModule(manager, &gmx_genbox, "genbox",
+ registerModule(manager, &gmx_solvate, "solvate",
"Solvate a system");
+ registerModule(manager, &gmx_insert_molecules, "insert-molecules",
+ "Insert molecules into existing vacancies");
+ registerObsoleteTool(manager, "genbox");
registerModule(manager, &gmx_genconf, "genconf",
"Multiply a conformation in 'random' orientations");
registerModule(manager, &gmx_genion, "genion",
group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
group.addModule("protonate");
group.addModule("x2top");
- group.addModule("genbox");
+ group.addModule("solvate");
+ group.addModule("insert-molecules");
group.addModule("genconf");
group.addModule("genion");
group.addModule("genrestr");
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff