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46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/fileio/pdbio.h"
49 #include "gromacs/gmxlib/conformation_utilities.h"
50 #include "gromacs/gmxpreprocess/makeexclusiondistances.h"
51 #include "gromacs/math/functions.h"
52 #include "gromacs/math/units.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/pbcutil/boxutilities.h"
55 #include "gromacs/pbcutil/pbc.h"
56 #include "gromacs/selection/nbsearch.h"
57 #include "gromacs/topology/atomprop.h"
58 #include "gromacs/topology/atoms.h"
59 #include "gromacs/topology/atomsbuilder.h"
60 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/topology/topology.h"
62 #include "gromacs/utility/arraysize.h"
63 #include "gromacs/utility/cstringutil.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/futil.h"
66 #include "gromacs/utility/gmxassert.h"
67 #include "gromacs/utility/smalloc.h"
79 static void sort_molecule(t_atoms **atoms_solvt,
84 int atnr, i, j, moltp = 0, nrmoltypes, resi_o, resi_n, resnr;
88 fprintf(stderr, "Sorting configuration\n");
92 /* copy each residue from *atoms to a molecule in *molecule */
95 for (i = 0; i < atoms->nr; i++)
97 if ( (i == 0) || (atoms->atom[i].resind != atoms->atom[i-1].resind) )
99 /* see if this was a molecule type we haven't had yet: */
101 for (j = 0; (j < nrmoltypes) && (moltp == -1); j++)
103 /* moltypes is guaranteed to be allocated because otherwise
104 * nrmoltypes is 0. */
105 if (strcmp(*(atoms->resinfo[atoms->atom[i].resind].name), moltypes[j].name) == 0)
114 srenew(moltypes, nrmoltypes);
115 moltypes[moltp].name = *(atoms->resinfo[atoms->atom[i].resind].name);
117 while ((i+atnr < atoms->nr) &&
118 (atoms->atom[i].resind == atoms->atom[i+atnr].resind))
122 moltypes[moltp].natoms = atnr;
123 moltypes[moltp].nmol = 0;
125 moltypes[moltp].nmol++;
129 fprintf(stderr, "Found %d%s molecule type%s:\n",
130 nrmoltypes, nrmoltypes == 1 ? "" : " different", nrmoltypes == 1 ? "" : "s");
131 for (j = 0; j < nrmoltypes; j++)
135 moltypes[j].res0 = 0;
139 moltypes[j].res0 = moltypes[j-1].res0+moltypes[j-1].nmol;
141 fprintf(stderr, "%7s (%4d atoms): %5d residues\n",
142 moltypes[j].name, moltypes[j].natoms, moltypes[j].nmol);
145 /* if we have only 1 moleculetype, we don't have to sort */
148 /* find out which molecules should go where: */
149 moltypes[0].i = moltypes[0].i0 = 0;
150 for (j = 1; j < nrmoltypes; j++)
154 moltypes[j-1].i0+moltypes[j-1].natoms*moltypes[j-1].nmol;
157 /* now put them there: */
159 init_t_atoms(*newatoms, atoms->nr, FALSE);
160 (*newatoms)->nres = atoms->nres;
161 srenew((*newatoms)->resinfo, atoms->nres);
162 std::vector<RVec> newx(x->size());
163 std::vector<RVec> newv(v->size());
168 for (moltp = 0; moltp < nrmoltypes; moltp++)
171 while (i < atoms->nr)
173 resi_o = atoms->atom[i].resind;
174 if (strcmp(*atoms->resinfo[resi_o].name, moltypes[moltp].name) == 0)
176 /* Copy the residue info */
177 (*newatoms)->resinfo[resi_n] = atoms->resinfo[resi_o];
178 (*newatoms)->resinfo[resi_n].nr = resnr;
179 /* Copy the atom info */
182 (*newatoms)->atom[j] = atoms->atom[i];
183 (*newatoms)->atomname[j] = atoms->atomname[i];
184 (*newatoms)->atom[j].resind = resi_n;
185 copy_rvec((*x)[i], newx[j]);
188 copy_rvec((*v)[i], newv[j]);
193 while (i < atoms->nr && atoms->atom[i].resind == resi_o);
194 /* Increase the new residue counters */
200 /* Skip this residue */
205 while (i < atoms->nr && atoms->atom[i].resind == resi_o);
210 /* put them back into the original arrays and throw away temporary arrays */
212 *atoms_solvt = (*newatoms);
219 static void rm_res_pbc(const t_atoms *atoms, std::vector<RVec> *x, matrix box)
227 for (int n = 0; n < atoms->nr; n++)
229 if (!is_hydrogen(*(atoms->atomname[n])))
232 rvec_inc(xcg, (*x)[n]);
234 if ( (n+1 == atoms->nr) ||
235 (atoms->atom[n+1].resind != atoms->atom[n].resind) )
237 /* if nat==0 we have only hydrogens in the solvent,
238 we take last coordinate as cg */
242 copy_rvec((*x)[n], xcg);
244 svmul(1.0/nat, xcg, xcg);
245 for (int d = 0; d < DIM; d++)
249 for (int i = start; i <= n; i++)
251 (*x)[i][d] += box[d][d];
255 while (xcg[d] >= box[d][d])
257 for (int i = start; i <= n; i++)
259 (*x)[i][d] -= box[d][d];
272 * Generates a solvent configuration of desired size by stacking solvent boxes.
274 * \param[in,out] atoms Solvent atoms.
275 * \param[in,out] x Solvent positions.
276 * \param[in,out] v Solvent velocities (`*v` can be NULL).
277 * \param[in,out] r Solvent exclusion radii.
278 * \param[in] box Initial solvent box.
279 * \param[in] boxTarget Target box size.
281 * The solvent box of desired size is created by stacking the initial box in
282 * the smallest k*l*m array that covers the box, and then removing any residue
283 * where all atoms are outside the target box (with a small margin).
284 * This function does not remove overlap between solvent atoms across the
287 * Note that the input configuration should be in the rectangular unit cell and
288 * have whole residues.
290 static void replicateSolventBox(t_atoms *atoms, std::vector<RVec> *x,
291 std::vector<RVec> *v, std::vector<real> *r,
292 const matrix box, const matrix boxTarget)
294 // Calculate the box multiplication factors.
297 for (int i = 0; i < DIM; ++i)
300 while (n_box[i] * box[i][i] < boxTarget[i][i])
306 fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n",
307 n_box[XX], n_box[YY], n_box[ZZ]);
309 // Create arrays for storing the generated system (cannot be done in-place
310 // in case the target box is smaller than the original in one dimension,
313 init_t_atoms(&newAtoms, 0, FALSE);
314 gmx::AtomsBuilder builder(&newAtoms, nullptr);
315 builder.reserve(atoms->nr * nmol, atoms->nres * nmol);
316 std::vector<RVec> newX(atoms->nr * nmol);
317 std::vector<RVec> newV(!v->empty() ? atoms->nr * nmol : 0);
318 std::vector<real> newR(atoms->nr * nmol);
320 const real maxRadius = *std::max_element(r->begin(), r->end());
322 for (int i = 0; i < DIM; ++i)
324 // The code below is only interested about the box diagonal.
325 boxWithMargin[i] = boxTarget[i][i] + 3*maxRadius;
328 for (int ix = 0; ix < n_box[XX]; ++ix)
331 delta[XX] = ix*box[XX][XX];
332 for (int iy = 0; iy < n_box[YY]; ++iy)
334 delta[YY] = iy*box[YY][YY];
335 for (int iz = 0; iz < n_box[ZZ]; ++iz)
337 delta[ZZ] = iz*box[ZZ][ZZ];
338 bool bKeepResidue = false;
339 for (int i = 0; i < atoms->nr; ++i)
341 const int newIndex = builder.currentAtomCount();
342 bool bKeepAtom = true;
343 for (int m = 0; m < DIM; ++m)
345 const real newCoord = delta[m] + (*x)[i][m];
346 bKeepAtom = bKeepAtom && (newCoord < boxWithMargin[m]);
347 newX[newIndex][m] = newCoord;
349 bKeepResidue = bKeepResidue || bKeepAtom;
352 copy_rvec((*v)[i], newV[newIndex]);
354 newR[newIndex] = (*r)[i];
355 builder.addAtom(*atoms, i);
356 if (i == atoms->nr - 1
357 || atoms->atom[i+1].resind != atoms->atom[i].resind)
361 builder.finishResidue(atoms->resinfo[atoms->atom[i].resind]);
365 builder.discardCurrentResidue();
367 // Reset state for the next residue.
368 bKeepResidue = false;
375 sfree(atoms->atomname);
376 sfree(atoms->resinfo);
377 atoms->nr = newAtoms.nr;
378 atoms->nres = newAtoms.nres;
379 atoms->atom = newAtoms.atom;
380 atoms->atomname = newAtoms.atomname;
381 atoms->resinfo = newAtoms.resinfo;
383 newX.resize(atoms->nr);
387 newV.resize(atoms->nr);
390 newR.resize(atoms->nr);
393 fprintf(stderr, "Solvent box contains %d atoms in %d residues\n",
394 atoms->nr, atoms->nres);
398 * Removes overlap of solvent atoms across the edges.
400 * \param[in,out] atoms Solvent atoms.
401 * \param[in,out] x Solvent positions.
402 * \param[in,out] v Solvent velocities (can be empty).
403 * \param[in,out] r Solvent exclusion radii.
404 * \param[in] pbc PBC information.
406 * Solvent residues that lay on the edges that do not touch the origin are
407 * removed if they overlap with other solvent atoms across the PBC.
408 * This is done in this way as the assumption is that the input solvent
409 * configuration is already equilibrated, and so does not contain any
410 * undesirable overlap. The only overlap that should be removed is caused by
411 * cutting the box in half in replicateSolventBox() and leaving a margin of
412 * solvent outside those box edges; these atoms can then overlap with those on
413 * the opposite box edge in a way that is not part of the pre-equilibrated
416 static void removeSolventBoxOverlap(t_atoms *atoms, std::vector<RVec> *x,
417 std::vector<RVec> *v, std::vector<real> *r,
420 gmx::AtomsRemover remover(*atoms);
422 // TODO: We could limit the amount of pairs searched significantly,
423 // since we are only interested in pairs where the positions are on
425 const real maxRadius = *std::max_element(r->begin(), r->end());
426 gmx::AnalysisNeighborhood nb;
427 nb.setCutoff(2*maxRadius);
428 gmx::AnalysisNeighborhoodPositions pos(*x);
429 gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
430 gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
431 gmx::AnalysisNeighborhoodPair pair;
432 while (pairSearch.findNextPair(&pair))
434 const int i1 = pair.refIndex();
435 const int i2 = pair.testIndex();
436 if (remover.isMarked(i2))
438 pairSearch.skipRemainingPairsForTestPosition();
441 if (remover.isMarked(i1) || atoms->atom[i1].resind == atoms->atom[i2].resind)
445 if (pair.distance2() < gmx::square((*r)[i1] + (*r)[i2]))
448 rvec_sub((*x)[i2], (*x)[i1], dx);
449 bool bCandidate1 = false, bCandidate2 = false;
450 // To satisfy Clang static analyzer.
451 GMX_ASSERT(pbc.ndim_ePBC <= DIM, "Too many periodic dimensions");
452 for (int d = 0; d < pbc.ndim_ePBC; ++d)
454 // If the distance in some dimension is larger than the
455 // cutoff, then it means that the distance has been computed
456 // over the PBC. Mark the position with a larger coordinate
457 // for potential removal.
458 if (dx[d] > maxRadius)
462 else if (dx[d] < -maxRadius)
467 // Only mark one of the positions for removal if both were
469 if (bCandidate2 && (!bCandidate1 || i2 > i1))
471 remover.markResidue(*atoms, i2, true);
472 pairSearch.skipRemainingPairsForTestPosition();
474 else if (bCandidate1)
476 remover.markResidue(*atoms, i1, true);
481 remover.removeMarkedElements(x);
484 remover.removeMarkedElements(v);
486 remover.removeMarkedElements(r);
487 const int originalAtomCount = atoms->nr;
488 remover.removeMarkedAtoms(atoms);
489 fprintf(stderr, "Removed %d solvent atoms due to solvent-solvent overlap\n",
490 originalAtomCount - atoms->nr);
494 * Remove all solvent molecules outside a give radius from the solute.
496 * \param[in,out] atoms Solvent atoms.
497 * \param[in,out] x_solvent Solvent positions.
498 * \param[in,out] v_solvent Solvent velocities.
499 * \param[in,out] r Atomic exclusion radii.
500 * \param[in] pbc PBC information.
501 * \param[in] x_solute Solute positions.
502 * \param[in] rshell The radius outside the solute molecule.
504 static void removeSolventOutsideShell(t_atoms *atoms,
505 std::vector<RVec> *x_solvent,
506 std::vector<RVec> *v_solvent,
507 std::vector<real> *r,
509 const std::vector<RVec> &x_solute,
512 gmx::AtomsRemover remover(*atoms);
513 gmx::AnalysisNeighborhood nb;
514 nb.setCutoff(rshell);
515 gmx::AnalysisNeighborhoodPositions posSolute(x_solute);
516 gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, posSolute);
517 gmx::AnalysisNeighborhoodPositions pos(*x_solvent);
518 gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
519 gmx::AnalysisNeighborhoodPair pair;
523 // Now put back those within the shell without checking for overlap
524 while (pairSearch.findNextPair(&pair))
526 remover.markResidue(*atoms, pair.testIndex(), false);
527 pairSearch.skipRemainingPairsForTestPosition();
529 remover.removeMarkedElements(x_solvent);
530 if (!v_solvent->empty())
532 remover.removeMarkedElements(v_solvent);
534 remover.removeMarkedElements(r);
535 const int originalAtomCount = atoms->nr;
536 remover.removeMarkedAtoms(atoms);
537 fprintf(stderr, "Removed %d solvent atoms more than %f nm from solute.\n",
538 originalAtomCount - atoms->nr, rshell);
542 * Removes solvent molecules that overlap with the solute.
544 * \param[in,out] atoms Solvent atoms.
545 * \param[in,out] x Solvent positions.
546 * \param[in,out] v Solvent velocities (can be empty).
547 * \param[in,out] r Solvent exclusion radii.
548 * \param[in] pbc PBC information.
549 * \param[in] x_solute Solute positions.
550 * \param[in] r_solute Solute exclusion radii.
552 static void removeSolventOverlappingWithSolute(t_atoms *atoms,
553 std::vector<RVec> *x,
554 std::vector<RVec> *v,
555 std::vector<real> *r,
557 const std::vector<RVec> &x_solute,
558 const std::vector<real> &r_solute)
560 gmx::AtomsRemover remover(*atoms);
561 const real maxRadius1
562 = *std::max_element(r->begin(), r->end());
563 const real maxRadius2
564 = *std::max_element(r_solute.begin(), r_solute.end());
566 // Now check for overlap.
567 gmx::AnalysisNeighborhood nb;
568 gmx::AnalysisNeighborhoodPair pair;
569 nb.setCutoff(maxRadius1 + maxRadius2);
570 gmx::AnalysisNeighborhoodPositions posSolute(x_solute);
571 gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, posSolute);
572 gmx::AnalysisNeighborhoodPositions pos(*x);
573 gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
574 while (pairSearch.findNextPair(&pair))
576 if (remover.isMarked(pair.testIndex()))
578 pairSearch.skipRemainingPairsForTestPosition();
581 const real r1 = r_solute[pair.refIndex()];
582 const real r2 = (*r)[pair.testIndex()];
583 const bool bRemove = (pair.distance2() < gmx::square(r1 + r2));
584 remover.markResidue(*atoms, pair.testIndex(), bRemove);
587 remover.removeMarkedElements(x);
590 remover.removeMarkedElements(v);
592 remover.removeMarkedElements(r);
593 const int originalAtomCount = atoms->nr;
594 remover.removeMarkedAtoms(atoms);
595 fprintf(stderr, "Removed %d solvent atoms due to solute-solvent overlap\n",
596 originalAtomCount - atoms->nr);
600 * Removes a given number of solvent residues.
602 * \param[in,out] atoms Solvent atoms.
603 * \param[in,out] x Solvent positions.
604 * \param[in,out] v Solvent velocities (can be empty).
605 * \param[in] numberToRemove Number of residues to remove.
607 * This function is called last in the process of creating the solvent box,
608 * so it does not operate on the exclusion radii, as no code after this needs
611 static void removeExtraSolventMolecules(t_atoms *atoms, std::vector<RVec> *x,
612 std::vector<RVec> *v,
615 gmx::AtomsRemover remover(*atoms);
616 // TODO: It might be nicer to remove a random set of residues, but
617 // in practice this should give a roughly uniform spatial distribution.
618 const int stride = atoms->nr / numberToRemove;
619 for (int i = 0; i < numberToRemove; ++i)
621 int atomIndex = (i+1)*stride - 1;
622 while (remover.isMarked(atomIndex))
625 if (atomIndex == atoms->nr)
630 remover.markResidue(*atoms, atomIndex, true);
632 remover.removeMarkedElements(x);
635 remover.removeMarkedElements(v);
637 remover.removeMarkedAtoms(atoms);
640 static void add_solv(const char *filename, t_atoms *atoms,
642 std::vector<RVec> *x, std::vector<RVec> *v,
643 int ePBC, matrix box, AtomProperties *aps,
644 real defaultDistance, real scaleFactor,
645 real rshell, int max_sol)
647 gmx_mtop_t topSolvent;
648 std::vector<RVec> xSolvent, vSolvent;
649 matrix boxSolvent = {{ 0 }};
652 fprintf(stderr, "Reading solvent configuration\n");
653 bool bTprFileWasRead;
654 rvec *temporaryX = nullptr, *temporaryV = nullptr;
655 readConfAndTopology(gmx::findLibraryFile(filename).c_str(), &bTprFileWasRead, &topSolvent,
656 &ePBCSolvent, &temporaryX, &temporaryV, boxSolvent);
657 t_atoms *atomsSolvent;
658 snew(atomsSolvent, 1);
659 *atomsSolvent = gmx_mtop_global_atoms(&topSolvent);
660 xSolvent.assign(temporaryX, temporaryX + topSolvent.natoms);
662 vSolvent.assign(temporaryV, temporaryV + topSolvent.natoms);
664 if (gmx::boxIsZero(boxSolvent))
666 gmx_fatal(FARGS, "No box information for solvent in %s, please use a properly formatted file\n",
669 if (0 == atomsSolvent->nr)
671 gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
673 fprintf(stderr, "\n");
675 /* initialise distance arrays for solvent configuration */
676 fprintf(stderr, "Initialising inter-atomic distances...\n");
677 const std::vector<real> exclusionDistances(
678 makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor));
679 std::vector<real> exclusionDistances_solvt(
680 makeExclusionDistances(atomsSolvent, aps, defaultDistance, scaleFactor));
682 /* generate a new solvent configuration */
683 fprintf(stderr, "Generating solvent configuration\n");
685 set_pbc(&pbc, ePBC, box);
686 if (!gmx::boxesAreEqual(boxSolvent, box))
688 if (TRICLINIC(boxSolvent))
690 gmx_fatal(FARGS, "Generating from non-rectangular solvent boxes is currently not supported.\n"
691 "You can try to pass the same box for -cp and -cs.");
693 /* apply pbc for solvent configuration for whole molecules */
694 rm_res_pbc(atomsSolvent, &xSolvent, boxSolvent);
695 replicateSolventBox(atomsSolvent, &xSolvent, &vSolvent, &exclusionDistances_solvt,
697 if (ePBC != epbcNONE)
699 removeSolventBoxOverlap(atomsSolvent, &xSolvent, &vSolvent, &exclusionDistances_solvt, pbc);
706 removeSolventOutsideShell(atomsSolvent, &xSolvent, &vSolvent,
707 &exclusionDistances_solvt, pbc, *x, rshell);
709 removeSolventOverlappingWithSolute(atomsSolvent, &xSolvent, &vSolvent,
710 &exclusionDistances_solvt, pbc, *x,
714 if (max_sol > 0 && atomsSolvent->nres > max_sol)
716 const int numberToRemove = atomsSolvent->nres - max_sol;
717 removeExtraSolventMolecules(atomsSolvent, &xSolvent, &vSolvent, numberToRemove);
720 /* Sort the solvent mixture, not the protein... */
721 t_atoms *newatoms = nullptr;
722 // The sort_molecule function does something creative with the
723 // t_atoms pointers. We need to make sure we neither leak, nor
724 // double-free, so make a shallow pointer that is fine for it to
726 t_atoms *sortedAtomsSolvent = atomsSolvent;
727 sort_molecule(&sortedAtomsSolvent, &newatoms, &xSolvent, &vSolvent);
729 // Merge the two configurations.
730 x->insert(x->end(), xSolvent.begin(), xSolvent.end());
733 v->insert(v->end(), vSolvent.begin(), vSolvent.end());
736 gmx::AtomsBuilder builder(atoms, symtab);
737 builder.mergeAtoms(*sortedAtomsSolvent);
739 fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
740 atomsSolvent->nr, atomsSolvent->nres);
749 done_atom(atomsSolvent);
754 static void update_top(t_atoms *atoms,
755 int firstSolventResidueIndex,
762 char buf[STRLEN*2], buf2[STRLEN], *temp;
763 const char *topinout;
770 int nsol = atoms->nres - firstSolventResidueIndex;
773 for (i = 0; (i < atoms->nr); i++)
775 aps->setAtomProperty(epropMass,
776 std::string(*atoms->resinfo[atoms->atom[i].resind].name),
777 std::string(*atoms->atomname[i]), &mm);
783 fprintf(stderr, "Volume : %10g (nm^3)\n", vol);
784 fprintf(stderr, "Density : %10g (g/l)\n",
785 (mtot*1e24)/(AVOGADRO*vol));
786 fprintf(stderr, "Number of solvent molecules: %5d \n\n", nsol);
788 /* open topology file and append sol molecules */
789 topinout = ftp2fn(efTOP, NFILE, fnm);
790 if (ftp2bSet(efTOP, NFILE, fnm) )
792 char temporary_filename[STRLEN];
793 strncpy(temporary_filename, "temp.topXXXXXX", STRLEN);
795 fprintf(stderr, "Processing topology\n");
796 fpin = gmx_ffopen(topinout, "r");
797 fpout = gmx_fopen_temporary(temporary_filename);
800 while (fgets(buf, STRLEN, fpin))
804 if ((temp = strchr(buf2, '\n')) != nullptr)
812 if ((temp = strchr(buf2, '\n')) != nullptr)
817 if (buf2[strlen(buf2)-1] == ']')
819 buf2[strlen(buf2)-1] = '\0';
822 bSystem = (gmx_strcasecmp(buf2, "system") == 0);
825 else if (bSystem && nsol && (buf[0] != ';') )
827 /* if sol present, append "in water" to system name */
829 if (buf2[0] && (!strstr(buf2, " water")) )
831 sprintf(buf, "%s in water\n", buf2);
835 fprintf(fpout, "%s", buf);
839 // Add new solvent molecules to the topology
842 std::string currRes = *atoms->resinfo[firstSolventResidueIndex].name;
845 // Iterate through solvent molecules and increment a count until new resname found
846 for (int i = firstSolventResidueIndex; i < atoms->nres; i++)
848 if ((currRes == *atoms->resinfo[i].name))
854 // Change topology and restart count
855 fprintf(stdout, "Adding line for %d solvent molecules with resname (%s) to "
856 "topology file (%s)\n", resCount, currRes.c_str(), topinout);
857 fprintf(fpout, "%-15s %5d\n", currRes.c_str(), resCount);
858 currRes = *atoms->resinfo[i].name;
862 // One more print needed for last residue type
863 fprintf(stdout, "Adding line for %d solvent molecules with resname (%s) to "
864 "topology file (%s)\n", resCount, currRes.c_str(), topinout);
865 fprintf(fpout, "%-15s %5d\n", currRes.c_str(), resCount);
868 make_backup(topinout);
869 gmx_file_rename(temporary_filename, topinout);
873 int gmx_solvate(int argc, char *argv[])
875 const char *desc[] = {
876 "[THISMODULE] can do one of 2 things:[PAR]",
878 "1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt].",
879 "Or specify [TT]-cs[tt] and [TT]-cp[tt] with a structure file with",
880 "a box, but without atoms.[PAR]",
882 "2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
883 "molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
884 "The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
885 "unless [TT]-box[tt] is set.",
886 "If you want the solute to be centered in the box,",
887 "the program [gmx-editconf] has sophisticated options",
888 "to change the box dimensions and center the solute.",
889 "Solvent molecules are removed from the box where the ",
890 "distance between any atom of the solute molecule(s) and any atom of ",
891 "the solvent molecule is less than the sum of the scaled van der Waals",
892 "radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
893 "Waals radii is read by the program, and the resulting radii scaled",
894 "by [TT]-scale[tt]. If radii are not found in the database, those",
895 "atoms are assigned the (pre-scaled) distance [TT]-radius[tt].",
896 "Note that the usefulness of those radii depends on the atom names,",
897 "and thus varies widely with force field.",
899 "The default solvent is Simple Point Charge water (SPC), with coordinates ",
900 "from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
901 "for other 3-site water models, since a short equibilibration will remove",
902 "the small differences between the models.",
903 "Other solvents are also supported, as well as mixed solvents. The",
904 "only restriction to solvent types is that a solvent molecule consists",
905 "of exactly one residue. The residue information in the coordinate",
906 "files is used, and should therefore be more or less consistent.",
907 "In practice this means that two subsequent solvent molecules in the ",
908 "solvent coordinate file should have different residue number.",
909 "The box of solute is built by stacking the coordinates read from",
910 "the coordinate file. This means that these coordinates should be ",
911 "equlibrated in periodic boundary conditions to ensure a good",
912 "alignment of molecules on the stacking interfaces.",
913 "The [TT]-maxsol[tt] option simply adds only the first [TT]-maxsol[tt]",
914 "solvent molecules and leaves out the rest that would have fitted",
915 "into the box. This can create a void that can cause problems later.",
916 "Choose your volume wisely.[PAR]",
918 "Setting [TT]-shell[tt] larger than zero will place a layer of water of",
919 "the specified thickness (nm) around the solute. Hint: it is a good",
920 "idea to put the protein in the center of a box first (using [gmx-editconf]).",
923 "Finally, [THISMODULE] will optionally remove lines from your topology file in ",
924 "which a number of solvent molecules is already added, and adds a ",
925 "line with the total number of solvent molecules in your coordinate file."
928 const char *bugs[] = {
929 "Molecules must be whole in the initial configurations.",
933 gmx_bool bProt, bBox;
934 const char *conf_prot, *confout;
937 { efSTX, "-cp", "protein", ffOPTRD },
938 { efSTX, "-cs", "spc216", ffLIBRD},
939 { efSTO, nullptr, nullptr, ffWRITE},
940 { efTOP, nullptr, nullptr, ffOPTRW},
942 #define NFILE asize(fnm)
944 real defaultDistance = 0.105, r_shell = 0, scaleFactor = 0.57;
945 rvec new_box = {0.0, 0.0, 0.0};
946 gmx_bool bReadV = FALSE;
948 int firstSolventResidueIndex = 0;
949 gmx_output_env_t *oenv;
951 { "-box", FALSE, etRVEC, {new_box},
952 "Box size (in nm)" },
953 { "-radius", FALSE, etREAL, {&defaultDistance},
954 "Default van der Waals distance"},
955 { "-scale", FALSE, etREAL, {&scaleFactor},
956 "Scale 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." },
957 { "-shell", FALSE, etREAL, {&r_shell},
958 "Thickness of optional water layer around solute" },
959 { "-maxsol", FALSE, etINT, {&max_sol},
960 "Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
961 { "-vel", FALSE, etBOOL, {&bReadV},
962 "Keep velocities from input solute and solvent" },
965 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
966 asize(desc), desc, asize(bugs), bugs, &oenv))
971 const char *solventFileName = opt2fn("-cs", NFILE, fnm);
972 bProt = opt2bSet("-cp", NFILE, fnm);
973 bBox = opt2parg_bSet("-box", asize(pa), pa);
978 gmx_fatal(FARGS, "When no solute (-cp) is specified, "
979 "a box size (-box) must be specified");
984 /* solute configuration data */
986 std::vector<RVec> x, v;
987 matrix box = {{ 0 }};
993 /* Generate a solute configuration */
994 conf_prot = opt2fn("-cp", NFILE, fnm);
995 fprintf(stderr, "Reading solute configuration%s\n",
996 bReadV ? " and velocities" : "");
997 bool bTprFileWasRead;
998 rvec *temporaryX = nullptr, *temporaryV = nullptr;
999 readConfAndTopology(conf_prot, &bTprFileWasRead, &top,
1000 &ePBC, &temporaryX, bReadV ? &temporaryV : nullptr, box);
1001 *atoms = gmx_mtop_global_atoms(&top);
1002 x.assign(temporaryX, temporaryX + top.natoms);
1006 v.assign(temporaryV, temporaryV + top.natoms);
1011 fprintf(stderr, "Note: no velocities found\n");
1015 fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
1020 firstSolventResidueIndex = atoms->nres;
1023 int ePBCForOutput = ePBC;
1026 ePBCForOutput = epbcXYZ;
1028 box[XX][XX] = new_box[XX];
1029 box[YY][YY] = new_box[YY];
1030 box[ZZ][ZZ] = new_box[ZZ];
1034 gmx_fatal(FARGS, "Undefined solute box.\nCreate one with gmx editconf "
1035 "or give explicit -box command line option");
1038 add_solv(solventFileName, atoms, &top.symtab, &x, &v, ePBCForOutput, box,
1039 &aps, defaultDistance, scaleFactor, r_shell, max_sol);
1041 /* write new configuration 1 to file confout */
1042 confout = ftp2fn(efSTO, NFILE, fnm);
1043 fprintf(stderr, "Writing generated configuration to %s\n", confout);
1044 const char *outputTitle = (bProt ? *top.name : "Generated by gmx solvate");
1045 write_sto_conf(confout, outputTitle, atoms, as_rvec_array(x.data()),
1046 !v.empty() ? as_rvec_array(v.data()) : nullptr, ePBCForOutput, box);
1048 /* print size of generated configuration */
1049 fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
1050 atoms->nr, atoms->nres);
1051 update_top(atoms, firstSolventResidueIndex, box, NFILE, fnm, &aps);
1055 output_env_done(oenv);