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40 #include "gen_vsite.h"
53 #include "gromacs/fileio/pdbio.h"
54 #include "gromacs/gmxpreprocess/add_par.h"
55 #include "gromacs/gmxpreprocess/fflibutil.h"
56 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
57 #include "gromacs/gmxpreprocess/grompp_impl.h"
58 #include "gromacs/gmxpreprocess/notset.h"
59 #include "gromacs/gmxpreprocess/toputil.h"
60 #include "gromacs/math/functions.h"
61 #include "gromacs/math/units.h"
62 #include "gromacs/math/vec.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/topology/ifunc.h"
65 #include "gromacs/topology/residuetypes.h"
66 #include "gromacs/topology/symtab.h"
67 #include "gromacs/utility/basedefinitions.h"
68 #include "gromacs/utility/cstringutil.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/futil.h"
71 #include "gromacs/utility/real.h"
72 #include "gromacs/utility/smalloc.h"
74 #include "hackblock.h"
78 #define OPENDIR '[' /* starting sign for directive */
79 #define CLOSEDIR ']' /* ending sign for directive */
81 /*! \libinternal \brief
82 * The configuration describing a virtual site.
84 struct VirtualSiteConfiguration
87 * Explicit constructor.
89 * \param[in] type Atomtype for vsite configuration.
90 * \param[in] planar Is the input conf planar.
91 * \param[in] nhyd How many hydrogens are in the configuration.
92 * \param[in] nextheavy Type of bonded heavy atom.
93 * \param[in] dummy What kind of dummy is used in the vsite.
95 explicit VirtualSiteConfiguration(const std::string& type,
98 const std::string& nextheavy,
99 const std::string& dummy) :
103 nextHeavyType(nextheavy),
107 //! Type for the XH3/XH2 atom.
108 std::string atomtype;
109 /*! \brief Is the configuration planar?
111 * If true, the atomtype above and the three connected
112 * ones are in a planar geometry. The two next entries
113 * are undefined in that case.
115 bool isplanar = false;
116 //! cnumber of connected hydrogens.
118 //! Type for the heavy atom bonded to XH2/XH3.
119 std::string nextHeavyType;
120 //! The type of MNH* or MCH3* dummy mass to use.
121 std::string dummyMass;
125 /*!\libinternal \brief
126 * Virtual site topology datastructure.
128 * Structure to represent average bond and angles values in vsite aromatic
129 * residues. Note that these are NOT necessarily the bonds and angles from the
130 * forcefield; many forcefields (like Amber, OPLS) have some inherent strain in
131 * 5-rings (i.e. the sum of angles is !=540, but impropers keep it planar)
133 struct VirtualSiteTopology
136 * Explicit constructor
138 * \param[in] name Residue name.
140 explicit VirtualSiteTopology(const std::string& name) : resname(name) {}
143 //! Helper struct for single bond in virtual site.
144 struct VirtualSiteBond
147 * Explicit constructor
149 * \param[in] a1 First atom name.
150 * \param[in] a2 Second atom name.
151 * \param[in] v Value for distance.
153 VirtualSiteBond(const std::string& a1, const std::string& a2, real v) :
163 //! Distance value between atoms.
166 //! Container of all bonds in virtual site.
167 std::vector<VirtualSiteBond> bond;
168 //! Helper struct for single angle in virtual site.
169 struct VirtualSiteAngle
172 * Explicit constructor
174 * \param[in] a1 First atom name.
175 * \param[in] a2 Second atom name.
176 * \param[in] a3 Third atom name.
177 * \param[in] v Value for angle.
179 VirtualSiteAngle(const std::string& a1, const std::string& a2, const std::string& a3, real v) :
195 //! Container for all angles in virtual site.
196 std::vector<VirtualSiteAngle> angle;
214 typedef char t_dirname[STRLEN];
216 static const t_dirname ddb_dirnames[DDB_DIR_NR] = { "CH3", "NH3", "NH2", "PHE", "TYR",
217 "TRP", "HISA", "HISB", "HISH" };
219 static int ddb_name2dir(char* name)
221 /* Translate a directive name to the number of the directive.
222 * HID/HIE/HIP names are translated to the ones we use in Gromacs.
229 for (i = 0; i < DDB_DIR_NR && index < 0; i++)
231 if (!gmx_strcasecmp(name, ddb_dirnames[i]))
241 static void read_vsite_database(const char* ddbname,
242 std::vector<VirtualSiteConfiguration>* vsiteconflist,
243 std::vector<VirtualSiteTopology>* vsitetoplist)
245 /* This routine is a quick hack to fix the problem with hardcoded atomtypes
246 * and aromatic vsite parameters by reading them from a ff???.vsd file.
248 * The file can contain sections [ NH3 ], [ CH3 ], [ NH2 ], and ring residue names.
249 * For the NH3 and CH3 section each line has three fields. The first is the atomtype
250 * (nb: not bonded type) of the N/C atom to be replaced, the second field is
251 * the type of the next heavy atom it is bonded to, and the third field the type
252 * of dummy mass that will be used for this group.
254 * If the NH2 group planar (sp2 N) a different vsite construct is used, so in this
255 * case the second field should just be the word planar.
262 char s1[MAXNAME], s2[MAXNAME], s3[MAXNAME], s4[MAXNAME];
264 gmx::FilePtr ddb = gmx::openLibraryFile(ddbname);
268 while (fgets2(pline, STRLEN - 2, ddb.get()) != nullptr)
270 strip_comment(pline);
272 if (strlen(pline) > 0)
274 if (pline[0] == OPENDIR)
276 strncpy(dirstr, pline + 1, STRLEN - 2);
277 if ((ch = strchr(dirstr, CLOSEDIR)) != nullptr)
283 if (!gmx_strcasecmp(dirstr, "HID") || !gmx_strcasecmp(dirstr, "HISD"))
285 sprintf(dirstr, "HISA");
287 else if (!gmx_strcasecmp(dirstr, "HIE") || !gmx_strcasecmp(dirstr, "HISE"))
289 sprintf(dirstr, "HISB");
291 else if (!gmx_strcasecmp(dirstr, "HIP"))
293 sprintf(dirstr, "HISH");
296 curdir = ddb_name2dir(dirstr);
299 gmx_fatal(FARGS, "Invalid directive %s in vsite database %s", dirstr, ddbname);
307 gmx_fatal(FARGS, "First entry in vsite database must be a directive.\n");
312 int numberOfSites = sscanf(pline, "%s%s%s", s1, s2, s3);
313 std::string s1String = s1;
314 std::string s2String = s2;
315 std::string s3String = s3;
316 if (numberOfSites < 3 && gmx::equalCaseInsensitive(s2String, "planar"))
318 VirtualSiteConfiguration newVsiteConf(s1String, true, 2, "0", "0");
319 vsiteconflist->push_back(newVsiteConf);
321 else if (numberOfSites == 3)
323 VirtualSiteConfiguration newVsiteConf(s1String, false, -1, s2String, s3String);
324 if (curdir == DDB_NH2)
326 newVsiteConf.nHydrogens = 2;
330 newVsiteConf.nHydrogens = 3;
332 vsiteconflist->push_back(newVsiteConf);
336 gmx_fatal(FARGS, "Not enough directives in vsite database line: %s\n", pline);
347 const auto found = std::find_if(
348 vsitetoplist->begin(), vsitetoplist->end(), [&dirstr](const auto& entry) {
349 return gmx::equalCaseInsensitive(dirstr, entry.resname);
351 /* Allocate a new topology entry if this is a new residue */
352 if (found == vsitetoplist->end())
354 vsitetoplist->push_back(VirtualSiteTopology(dirstr));
356 int numberOfSites = sscanf(pline, "%s%s%s%s", s1, s2, s3, s4);
357 std::string s1String = s1;
358 std::string s2String = s2;
359 std::string s3String = s3;
361 if (numberOfSites == 3)
364 vsitetoplist->back().bond.emplace_back(s1String, s2String, strtod(s3, nullptr));
366 else if (numberOfSites == 4)
369 vsitetoplist->back().angle.emplace_back(
370 s1String, s2String, s3String, strtod(s4, nullptr));
376 "Need 3 or 4 values to specify bond/angle values in %s: %s\n",
384 "Didnt find a case for directive %s in read_vsite_database\n",
392 static int nitrogen_is_planar(gmx::ArrayRef<const VirtualSiteConfiguration> vsiteconflist,
393 const std::string& atomtype)
395 /* Return 1 if atomtype exists in database list and is planar, 0 if not,
396 * and -1 if not found.
400 std::find_if(vsiteconflist.begin(), vsiteconflist.end(), [&atomtype](const auto& entry) {
401 return (gmx::equalCaseInsensitive(entry.atomtype, atomtype) && entry.nHydrogens == 2);
403 if (found != vsiteconflist.end())
405 res = static_cast<int>(found->isplanar);
415 static std::string get_dummymass_name(gmx::ArrayRef<const VirtualSiteConfiguration> vsiteconflist,
416 const std::string& atom,
417 const std::string& nextheavy)
419 /* Return the dummy mass name if found, or NULL if not set in ddb database */
420 const auto found = std::find_if(
421 vsiteconflist.begin(), vsiteconflist.end(), [&atom, &nextheavy](const auto& entry) {
422 return (gmx::equalCaseInsensitive(atom, entry.atomtype)
423 && gmx::equalCaseInsensitive(nextheavy, entry.nextHeavyType));
425 if (found != vsiteconflist.end())
427 return found->dummyMass;
436 static real get_ddb_bond(gmx::ArrayRef<const VirtualSiteTopology> vsitetop,
437 const std::string& res,
438 const std::string& atom1,
439 const std::string& atom2)
441 const auto found = std::find_if(vsitetop.begin(), vsitetop.end(), [&res](const auto& entry) {
442 return gmx::equalCaseInsensitive(res, entry.resname);
445 if (found == vsitetop.end())
447 gmx_fatal(FARGS, "No vsite information for residue %s found in vsite database.\n", res.c_str());
449 const auto foundBond =
450 std::find_if(found->bond.begin(), found->bond.end(), [&atom1, &atom2](const auto& entry) {
451 return ((atom1 == entry.atom1 && atom2 == entry.atom2)
452 || (atom1 == entry.atom2 && atom2 == entry.atom1));
454 if (foundBond == found->bond.end())
457 "Couldnt find bond %s-%s for residue %s in vsite database.\n",
463 return foundBond->value;
467 static real get_ddb_angle(gmx::ArrayRef<const VirtualSiteTopology> vsitetop,
468 const std::string& res,
469 const std::string& atom1,
470 const std::string& atom2,
471 const std::string& atom3)
473 const auto found = std::find_if(vsitetop.begin(), vsitetop.end(), [&res](const auto& entry) {
474 return gmx::equalCaseInsensitive(res, entry.resname);
477 if (found == vsitetop.end())
479 gmx_fatal(FARGS, "No vsite information for residue %s found in vsite database.\n", res.c_str());
481 const auto foundAngle = std::find_if(
482 found->angle.begin(), found->angle.end(), [&atom1, &atom2, &atom3](const auto& entry) {
483 return ((atom1 == entry.atom1 && atom2 == entry.atom2 && atom3 == entry.atom3)
484 || (atom1 == entry.atom3 && atom2 == entry.atom2 && atom3 == entry.atom1)
485 || (atom1 == entry.atom2 && atom2 == entry.atom1 && atom3 == entry.atom3)
486 || (atom1 == entry.atom3 && atom2 == entry.atom1 && atom3 == entry.atom2));
489 if (foundAngle == found->angle.end())
492 "Couldnt find angle %s-%s-%s for residue %s in vsite database.\n",
499 return foundAngle->value;
503 static void count_bonds(int atom,
504 InteractionsOfType* psb,
513 int heavy, other, nrb, nrH, nrhv;
515 /* find heavy atom bound to this hydrogen */
517 for (auto parm = psb->interactionTypes.begin();
518 (parm != psb->interactionTypes.end()) && (heavy == NOTSET);
521 if (parm->ai() == atom)
525 else if (parm->aj() == atom)
532 gmx_fatal(FARGS, "unbound hydrogen atom %d", atom + 1);
534 /* find all atoms bound to heavy atom */
539 for (const auto& parm : psb->interactionTypes)
541 if (parm.ai() == heavy)
545 else if (parm.aj() == heavy)
552 if (is_hydrogen(*(atomname[other])))
559 heavies[nrhv] = other;
572 print_bonds(FILE* fp, int o2n[], int nrHatoms, const int Hatoms[], int Heavy, int nrheavies, const int heavies[])
576 fprintf(fp, "Found: %d Hatoms: ", nrHatoms);
577 for (i = 0; i < nrHatoms; i++)
579 fprintf(fp, " %d", o2n[Hatoms[i]] + 1);
581 fprintf(fp, "; %d Heavy atoms: %d", nrheavies + 1, o2n[Heavy] + 1);
582 for (i = 0; i < nrheavies; i++)
584 fprintf(fp, " %d", o2n[heavies[i]] + 1);
589 static int get_atype(int atom, t_atoms* at, gmx::ArrayRef<const PreprocessResidue> rtpFFDB, ResidueType* rt)
594 if (at->atom[atom].m != 0.0F)
596 type = at->atom[atom].type;
600 /* get type from rtpFFDB */
601 auto localPpResidue = getDatabaseEntry(*(at->resinfo[at->atom[atom].resind].name), rtpFFDB);
602 bNterm = rt->namedResidueHasType(*(at->resinfo[at->atom[atom].resind].name), "Protein")
603 && (at->atom[atom].resind == 0);
604 int j = search_jtype(*localPpResidue, *(at->atomname[atom]), bNterm);
605 type = localPpResidue->atom[j].type;
610 static int vsite_nm2type(const char* name, PreprocessingAtomTypes* atype)
612 auto tp = atype->atomTypeFromName(name);
615 gmx_fatal(FARGS, "Dummy mass type (%s) not found in atom type database", name);
621 static real get_amass(int atom, t_atoms* at, gmx::ArrayRef<const PreprocessResidue> rtpFFDB, ResidueType* rt)
626 if (at->atom[atom].m != 0.0F)
628 mass = at->atom[atom].m;
632 /* get mass from rtpFFDB */
633 auto localPpResidue = getDatabaseEntry(*(at->resinfo[at->atom[atom].resind].name), rtpFFDB);
634 bNterm = rt->namedResidueHasType(*(at->resinfo[at->atom[atom].resind].name), "Protein")
635 && (at->atom[atom].resind == 0);
636 int j = search_jtype(*localPpResidue, *(at->atomname[atom]), bNterm);
637 mass = localPpResidue->atom[j].m;
642 static void my_add_param(InteractionsOfType* plist, int ai, int aj, real b)
644 static real c[MAXFORCEPARAM] = { NOTSET, NOTSET, NOTSET, NOTSET, NOTSET, NOTSET };
647 add_param(plist, ai, aj, c, nullptr);
650 static void add_vsites(gmx::ArrayRef<InteractionsOfType> plist,
658 int other, moreheavy;
660 for (int i = 0; i < nrHatoms; i++)
662 int ftype = vsite_type[Hatoms[i]];
663 /* Errors in setting the vsite_type should really be caugth earlier,
664 * because here it's not possible to print any useful error message.
665 * But it's still better to print a message than to segfault.
669 gmx_incons("Undetected error in setting up virtual sites");
671 bool bSwapParity = (ftype < 0);
672 vsite_type[Hatoms[i]] = ftype = abs(ftype);
673 if (ftype == F_BONDS)
675 if ((nrheavies != 1) && (nrHatoms != 1))
678 "cannot make constraint in add_vsites for %d heavy "
679 "atoms and %d hydrogen atoms",
683 my_add_param(&(plist[F_CONSTRNC]), Hatoms[i], heavies[0], NOTSET);
695 "Not enough heavy atoms (%d) for %s (min 3)",
697 interaction_function[vsite_type[Hatoms[i]]].name);
699 add_vsite3_atoms(&plist[ftype], Hatoms[i], Heavy, heavies[0], heavies[1], bSwapParity);
705 moreheavy = heavies[1];
709 /* find more heavy atoms */
710 other = moreheavy = NOTSET;
711 for (auto parm = plist[F_BONDS].interactionTypes.begin();
712 (parm != plist[F_BONDS].interactionTypes.end()) && (moreheavy == NOTSET);
715 if (parm->ai() == heavies[0])
719 else if (parm->aj() == heavies[0])
723 if ((other != NOTSET) && (other != Heavy))
728 if (moreheavy == NOTSET)
730 gmx_fatal(FARGS, "Unbound molecule part %d-%d", Heavy + 1, Hatoms[0] + 1);
733 add_vsite3_atoms(&plist[ftype], Hatoms[i], Heavy, heavies[0], moreheavy, bSwapParity);
741 "Not enough heavy atoms (%d) for %s (min 4)",
743 interaction_function[vsite_type[Hatoms[i]]].name);
745 add_vsite4_atoms(&plist[ftype], Hatoms[0], Heavy, heavies[0], heavies[1], heavies[2]);
750 "can't use add_vsites for interaction function %s",
751 interaction_function[vsite_type[Hatoms[i]]].name);
757 #define ANGLE_6RING (DEG2RAD * 120)
759 /* cosine rule: a^2 = b^2 + c^2 - 2 b c cos(alpha) */
760 /* get a^2 when a, b and alpha are given: */
761 #define cosrule(b, c, alpha) (gmx::square(b) + gmx::square(c) - 2 * (b) * (c)*std::cos(alpha))
762 /* get cos(alpha) when a, b and c are given: */
763 #define acosrule(a, b, c) ((gmx::square(b) + gmx::square(c) - gmx::square(a)) / (2 * (b) * (c)))
765 static int gen_vsites_6ring(t_atoms* at,
767 gmx::ArrayRef<InteractionsOfType> plist,
775 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
793 real a, b, dCGCE, tmp1, tmp2, mtot, mG, mrest;
795 /* CG, CE1 and CE2 stay and each get a part of the total mass,
796 * so the c-o-m stays the same.
803 gmx_incons("Generating vsites on 6-rings");
807 /* constraints between CG, CE1 and CE2: */
808 dCGCE = std::sqrt(cosrule(bond_cc, bond_cc, ANGLE_6RING));
809 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atCE1], dCGCE);
810 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atCE2], dCGCE);
811 my_add_param(&(plist[F_CONSTRNC]), ats[atCE1], ats[atCE2], dCGCE);
813 /* rest will be vsite3 */
816 for (i = 0; i < (bDoZ ? atNR : atHZ); i++)
818 mtot += at->atom[ats[i]].m;
819 if (i != atCG && i != atCE1 && i != atCE2 && (bDoZ || (i != atHZ && i != atCZ)))
821 at->atom[ats[i]].m = at->atom[ats[i]].mB = 0;
822 (*vsite_type)[ats[i]] = F_VSITE3;
826 /* Distribute mass so center-of-mass stays the same.
827 * The center-of-mass in the call is defined with x=0 at
828 * the CE1-CE2 bond and y=0 at the line from CG to the middle of CE1-CE2 bond.
830 xCG = -bond_cc + bond_cc * std::cos(ANGLE_6RING);
832 mG = at->atom[ats[atCG]].m = at->atom[ats[atCG]].mB = xcom * mtot / xCG;
834 at->atom[ats[atCE1]].m = at->atom[ats[atCE1]].mB = at->atom[ats[atCE2]].m =
835 at->atom[ats[atCE2]].mB = mrest / 2;
837 /* vsite3 construction: r_d = r_i + a r_ij + b r_ik */
838 tmp1 = dCGCE * std::sin(ANGLE_6RING * 0.5);
839 tmp2 = bond_cc * std::cos(0.5 * ANGLE_6RING) + tmp1;
841 a = b = -bond_ch / tmp1;
843 add_vsite3_param(&plist[F_VSITE3], ats[atHE1], ats[atCE1], ats[atCE2], ats[atCG], a, b);
844 add_vsite3_param(&plist[F_VSITE3], ats[atHE2], ats[atCE2], ats[atCE1], ats[atCG], a, b);
845 /* CD1, CD2 and CZ: */
847 add_vsite3_param(&plist[F_VSITE3], ats[atCD1], ats[atCE2], ats[atCE1], ats[atCG], a, b);
848 add_vsite3_param(&plist[F_VSITE3], ats[atCD2], ats[atCE1], ats[atCE2], ats[atCG], a, b);
851 add_vsite3_param(&plist[F_VSITE3], ats[atCZ], ats[atCG], ats[atCE1], ats[atCE2], a, b);
853 /* HD1, HD2 and HZ: */
854 a = b = (bond_ch + tmp2) / tmp1;
855 add_vsite3_param(&plist[F_VSITE3], ats[atHD1], ats[atCE2], ats[atCE1], ats[atCG], a, b);
856 add_vsite3_param(&plist[F_VSITE3], ats[atHD2], ats[atCE1], ats[atCE2], ats[atCG], a, b);
859 add_vsite3_param(&plist[F_VSITE3], ats[atHZ], ats[atCG], ats[atCE1], ats[atCE2], a, b);
865 static int gen_vsites_phe(t_atoms* at,
867 gmx::ArrayRef<InteractionsOfType> plist,
870 gmx::ArrayRef<const VirtualSiteTopology> vsitetop)
872 real bond_cc, bond_ch;
875 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
892 /* Aromatic rings have 6-fold symmetry, so we only need one bond length.
893 * (angle is always 120 degrees).
895 bond_cc = get_ddb_bond(vsitetop, "PHE", "CD1", "CE1");
896 bond_ch = get_ddb_bond(vsitetop, "PHE", "CD1", "HD1");
898 x[atCG] = -bond_cc + bond_cc * std::cos(ANGLE_6RING);
900 x[atHD1] = x[atCD1] + bond_ch * std::cos(ANGLE_6RING);
902 x[atHE1] = x[atCE1] - bond_ch * std::cos(ANGLE_6RING);
907 x[atCZ] = bond_cc * std::cos(0.5 * ANGLE_6RING);
908 x[atHZ] = x[atCZ] + bond_ch;
911 for (i = 0; i < atNR; i++)
913 xcom += x[i] * at->atom[ats[i]].m;
914 mtot += at->atom[ats[i]].m;
918 return gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, TRUE);
922 calc_vsite3_param(real xd, real yd, real xi, real yi, real xj, real yj, real xk, real yk, real* a, real* b)
924 /* determine parameters by solving the equation system, since we know the
925 * virtual site coordinates here.
927 real dx_ij, dx_ik, dy_ij, dy_ik;
934 *a = ((xd - xi) * dy_ik - dx_ik * (yd - yi)) / (dx_ij * dy_ik - dx_ik * dy_ij);
935 *b = (yd - yi - (*a) * dy_ij) / dy_ik;
939 static int gen_vsites_trp(PreprocessingAtomTypes* atype,
940 std::vector<gmx::RVec>* newx,
942 char*** newatomname[],
944 int* newvsite_type[],
948 gmx::ArrayRef<const gmx::RVec> x,
952 gmx::ArrayRef<InteractionsOfType> plist,
956 gmx::ArrayRef<const VirtualSiteTopology> vsitetop)
959 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
980 /* weights for determining the COM's of both rings (M1 and M2): */
981 real mw[NMASS][atNR] = { { 0, 1, 1, 1, 0.5, 1, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0 },
982 { 0, 0, 0, 0, 0.5, 0, 0, 0.5, 1, 1, 1, 1, 1, 1, 1, 1 } };
984 real xi[atNR], yi[atNR];
985 real xcom[NMASS], ycom[NMASS], alpha;
986 real b_CD2_CE2, b_NE1_CE2, b_CG_CD2, b_CH2_HH2, b_CE2_CZ2;
987 real b_NE1_HE1, b_CD2_CE3, b_CE3_CZ3, b_CB_CG;
988 real b_CZ2_CH2, b_CZ2_HZ2, b_CD1_HD1, b_CE3_HE3;
989 real b_CG_CD1, b_CZ3_HZ3;
990 real a_NE1_CE2_CD2, a_CE2_CD2_CG, a_CB_CG_CD2, a_CE2_CD2_CE3;
991 real a_CD2_CG_CD1, a_CE2_CZ2_HZ2, a_CZ2_CH2_HH2;
992 real a_CD2_CE2_CZ2, a_CD2_CE3_CZ3, a_CE3_CZ3_HZ3, a_CG_CD1_HD1;
993 real a_CE2_CZ2_CH2, a_HE1_NE1_CE2, a_CD2_CE3_HE3;
994 int atM[NMASS], tpM, i, i0, j, nvsite;
995 real mM[NMASS], dCBM1, dCBM2, dM1M2;
997 rvec r_ij, r_ik, t1, t2;
1000 if (atNR != nrfound)
1002 gmx_incons("atom types in gen_vsites_trp");
1004 /* Get geometry from database */
1005 b_CD2_CE2 = get_ddb_bond(vsitetop, "TRP", "CD2", "CE2");
1006 b_NE1_CE2 = get_ddb_bond(vsitetop, "TRP", "NE1", "CE2");
1007 b_CG_CD1 = get_ddb_bond(vsitetop, "TRP", "CG", "CD1");
1008 b_CG_CD2 = get_ddb_bond(vsitetop, "TRP", "CG", "CD2");
1009 b_CB_CG = get_ddb_bond(vsitetop, "TRP", "CB", "CG");
1010 b_CE2_CZ2 = get_ddb_bond(vsitetop, "TRP", "CE2", "CZ2");
1011 b_CD2_CE3 = get_ddb_bond(vsitetop, "TRP", "CD2", "CE3");
1012 b_CE3_CZ3 = get_ddb_bond(vsitetop, "TRP", "CE3", "CZ3");
1013 b_CZ2_CH2 = get_ddb_bond(vsitetop, "TRP", "CZ2", "CH2");
1015 b_CD1_HD1 = get_ddb_bond(vsitetop, "TRP", "CD1", "HD1");
1016 b_CZ2_HZ2 = get_ddb_bond(vsitetop, "TRP", "CZ2", "HZ2");
1017 b_NE1_HE1 = get_ddb_bond(vsitetop, "TRP", "NE1", "HE1");
1018 b_CH2_HH2 = get_ddb_bond(vsitetop, "TRP", "CH2", "HH2");
1019 b_CE3_HE3 = get_ddb_bond(vsitetop, "TRP", "CE3", "HE3");
1020 b_CZ3_HZ3 = get_ddb_bond(vsitetop, "TRP", "CZ3", "HZ3");
1022 a_NE1_CE2_CD2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "NE1", "CE2", "CD2");
1023 a_CE2_CD2_CG = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CD2", "CG");
1024 a_CB_CG_CD2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CB", "CG", "CD2");
1025 a_CD2_CG_CD1 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CG", "CD1");
1027 a_CE2_CD2_CE3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CD2", "CE3");
1028 a_CD2_CE2_CZ2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CE2", "CZ2");
1029 a_CD2_CE3_CZ3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CE3", "CZ3");
1030 a_CE3_CZ3_HZ3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE3", "CZ3", "HZ3");
1031 a_CZ2_CH2_HH2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CZ2", "CH2", "HH2");
1032 a_CE2_CZ2_HZ2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CZ2", "HZ2");
1033 a_CE2_CZ2_CH2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CZ2", "CH2");
1034 a_CG_CD1_HD1 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CG", "CD1", "HD1");
1035 a_HE1_NE1_CE2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "HE1", "NE1", "CE2");
1036 a_CD2_CE3_HE3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CE3", "HE3");
1038 /* Calculate local coordinates.
1039 * y-axis (x=0) is the bond CD2-CE2.
1040 * x-axis (y=0) is perpendicular to the bond CD2-CE2 and
1041 * intersects the middle of the bond.
1044 yi[atCD2] = -0.5 * b_CD2_CE2;
1047 yi[atCE2] = 0.5 * b_CD2_CE2;
1049 xi[atNE1] = -b_NE1_CE2 * std::sin(a_NE1_CE2_CD2);
1050 yi[atNE1] = yi[atCE2] - b_NE1_CE2 * std::cos(a_NE1_CE2_CD2);
1052 xi[atCG] = -b_CG_CD2 * std::sin(a_CE2_CD2_CG);
1053 yi[atCG] = yi[atCD2] + b_CG_CD2 * std::cos(a_CE2_CD2_CG);
1055 alpha = a_CE2_CD2_CG + M_PI - a_CB_CG_CD2;
1056 xi[atCB] = xi[atCG] - b_CB_CG * std::sin(alpha);
1057 yi[atCB] = yi[atCG] + b_CB_CG * std::cos(alpha);
1059 alpha = a_CE2_CD2_CG + a_CD2_CG_CD1 - M_PI;
1060 xi[atCD1] = xi[atCG] - b_CG_CD1 * std::sin(alpha);
1061 yi[atCD1] = yi[atCG] + b_CG_CD1 * std::cos(alpha);
1063 xi[atCE3] = b_CD2_CE3 * std::sin(a_CE2_CD2_CE3);
1064 yi[atCE3] = yi[atCD2] + b_CD2_CE3 * std::cos(a_CE2_CD2_CE3);
1066 xi[atCZ2] = b_CE2_CZ2 * std::sin(a_CD2_CE2_CZ2);
1067 yi[atCZ2] = yi[atCE2] - b_CE2_CZ2 * std::cos(a_CD2_CE2_CZ2);
1069 alpha = a_CE2_CD2_CE3 + a_CD2_CE3_CZ3 - M_PI;
1070 xi[atCZ3] = xi[atCE3] + b_CE3_CZ3 * std::sin(alpha);
1071 yi[atCZ3] = yi[atCE3] + b_CE3_CZ3 * std::cos(alpha);
1073 alpha = a_CD2_CE2_CZ2 + a_CE2_CZ2_CH2 - M_PI;
1074 xi[atCH2] = xi[atCZ2] + b_CZ2_CH2 * std::sin(alpha);
1075 yi[atCH2] = yi[atCZ2] - b_CZ2_CH2 * std::cos(alpha);
1078 alpha = a_CE2_CD2_CG + a_CD2_CG_CD1 - a_CG_CD1_HD1;
1079 xi[atHD1] = xi[atCD1] - b_CD1_HD1 * std::sin(alpha);
1080 yi[atHD1] = yi[atCD1] + b_CD1_HD1 * std::cos(alpha);
1082 alpha = a_NE1_CE2_CD2 + M_PI - a_HE1_NE1_CE2;
1083 xi[atHE1] = xi[atNE1] - b_NE1_HE1 * std::sin(alpha);
1084 yi[atHE1] = yi[atNE1] - b_NE1_HE1 * std::cos(alpha);
1086 alpha = a_CE2_CD2_CE3 + M_PI - a_CD2_CE3_HE3;
1087 xi[atHE3] = xi[atCE3] + b_CE3_HE3 * std::sin(alpha);
1088 yi[atHE3] = yi[atCE3] + b_CE3_HE3 * std::cos(alpha);
1090 alpha = a_CD2_CE2_CZ2 + M_PI - a_CE2_CZ2_HZ2;
1091 xi[atHZ2] = xi[atCZ2] + b_CZ2_HZ2 * std::sin(alpha);
1092 yi[atHZ2] = yi[atCZ2] - b_CZ2_HZ2 * std::cos(alpha);
1094 alpha = a_CD2_CE2_CZ2 + a_CE2_CZ2_CH2 - a_CZ2_CH2_HH2;
1095 xi[atHZ3] = xi[atCZ3] + b_CZ3_HZ3 * std::sin(alpha);
1096 yi[atHZ3] = yi[atCZ3] + b_CZ3_HZ3 * std::cos(alpha);
1098 alpha = a_CE2_CD2_CE3 + a_CD2_CE3_CZ3 - a_CE3_CZ3_HZ3;
1099 xi[atHH2] = xi[atCH2] + b_CH2_HH2 * std::sin(alpha);
1100 yi[atHH2] = yi[atCH2] - b_CH2_HH2 * std::cos(alpha);
1102 /* Calculate masses for each ring and put it on the dummy masses */
1103 for (j = 0; j < NMASS; j++)
1105 mM[j] = xcom[j] = ycom[j] = 0;
1107 for (i = 0; i < atNR; i++)
1111 for (j = 0; j < NMASS; j++)
1113 mM[j] += mw[j][i] * at->atom[ats[i]].m;
1114 xcom[j] += xi[i] * mw[j][i] * at->atom[ats[i]].m;
1115 ycom[j] += yi[i] * mw[j][i] * at->atom[ats[i]].m;
1119 for (j = 0; j < NMASS; j++)
1125 /* get dummy mass type */
1126 tpM = vsite_nm2type("MW", atype);
1127 /* make space for 2 masses: shift all atoms starting with CB */
1129 for (j = 0; j < NMASS; j++)
1131 atM[j] = i0 + *nadd + j;
1135 fprintf(stderr, "Inserting %d dummy masses at %d\n", NMASS, (*o2n)[i0] + 1);
1138 for (j = i0; j < at->nr; j++)
1140 (*o2n)[j] = j + *nadd;
1142 newx->resize(at->nr + *nadd);
1143 srenew(*newatom, at->nr + *nadd);
1144 srenew(*newatomname, at->nr + *nadd);
1145 srenew(*newvsite_type, at->nr + *nadd);
1146 srenew(*newcgnr, at->nr + *nadd);
1147 for (j = 0; j < NMASS; j++)
1149 (*newatomname)[at->nr + *nadd - 1 - j] = nullptr;
1152 /* Dummy masses will be placed at the center-of-mass in each ring. */
1154 /* calc initial position for dummy masses in real (non-local) coordinates.
1155 * Cheat by using the routine to calculate virtual site parameters. It is
1156 * much easier when we have the coordinates expressed in terms of
1159 rvec_sub(x[ats[atCB]], x[ats[atCG]], r_ij);
1160 rvec_sub(x[ats[atCD2]], x[ats[atCG]], r_ik);
1162 xcom[0], ycom[0], xi[atCG], yi[atCG], xi[atCB], yi[atCB], xi[atCD2], yi[atCD2], &a, &b);
1165 rvec_add(t1, t2, t1);
1166 rvec_add(t1, x[ats[atCG]], (*newx)[atM[0]]);
1169 xcom[1], ycom[1], xi[atCG], yi[atCG], xi[atCB], yi[atCB], xi[atCD2], yi[atCD2], &a, &b);
1172 rvec_add(t1, t2, t1);
1173 rvec_add(t1, x[ats[atCG]], (*newx)[atM[1]]);
1175 /* set parameters for the masses */
1176 for (j = 0; j < NMASS; j++)
1178 sprintf(name, "MW%d", j + 1);
1179 (*newatomname)[atM[j]] = put_symtab(symtab, name);
1180 (*newatom)[atM[j]].m = (*newatom)[atM[j]].mB = mM[j];
1181 (*newatom)[atM[j]].q = (*newatom)[atM[j]].qB = 0.0;
1182 (*newatom)[atM[j]].type = (*newatom)[atM[j]].typeB = tpM;
1183 (*newatom)[atM[j]].ptype = eptAtom;
1184 (*newatom)[atM[j]].resind = at->atom[i0].resind;
1185 (*newatom)[atM[j]].elem[0] = 'M';
1186 (*newatom)[atM[j]].elem[1] = '\0';
1187 (*newvsite_type)[atM[j]] = NOTSET;
1188 (*newcgnr)[atM[j]] = (*cgnr)[i0];
1190 /* renumber cgnr: */
1191 for (i = i0; i < at->nr; i++)
1196 /* constraints between CB, M1 and M2 */
1197 /* 'add_shift' says which atoms won't be renumbered afterwards */
1198 dCBM1 = std::hypot(xcom[0] - xi[atCB], ycom[0] - yi[atCB]);
1199 dM1M2 = std::hypot(xcom[0] - xcom[1], ycom[0] - ycom[1]);
1200 dCBM2 = std::hypot(xcom[1] - xi[atCB], ycom[1] - yi[atCB]);
1201 my_add_param(&(plist[F_CONSTRNC]), ats[atCB], add_shift + atM[0], dCBM1);
1202 my_add_param(&(plist[F_CONSTRNC]), ats[atCB], add_shift + atM[1], dCBM2);
1203 my_add_param(&(plist[F_CONSTRNC]), add_shift + atM[0], add_shift + atM[1], dM1M2);
1205 /* rest will be vsite3 */
1207 for (i = 0; i < atNR; i++)
1211 at->atom[ats[i]].m = at->atom[ats[i]].mB = 0;
1212 (*vsite_type)[ats[i]] = F_VSITE3;
1217 /* now define all vsites from M1, M2, CB, ie:
1218 r_d = r_M1 + a r_M1_M2 + b r_M1_CB */
1219 for (i = 0; i < atNR; i++)
1221 if ((*vsite_type)[ats[i]] == F_VSITE3)
1224 xi[i], yi[i], xcom[0], ycom[0], xcom[1], ycom[1], xi[atCB], yi[atCB], &a, &b);
1226 &plist[F_VSITE3], ats[i], add_shift + atM[0], add_shift + atM[1], ats[atCB], a, b);
1234 static int gen_vsites_tyr(PreprocessingAtomTypes* atype,
1235 std::vector<gmx::RVec>* newx,
1237 char*** newatomname[],
1239 int* newvsite_type[],
1243 gmx::ArrayRef<const gmx::RVec> x,
1247 gmx::ArrayRef<InteractionsOfType> plist,
1251 gmx::ArrayRef<const VirtualSiteTopology> vsitetop)
1253 int nvsite, i, i0, j, atM, tpM;
1254 real dCGCE, dCEOH, dCGM, tmp1, a, b;
1255 real bond_cc, bond_ch, bond_co, bond_oh, angle_coh;
1261 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
1279 /* CG, CE1, CE2 (as in general 6-ring) and OH and HH stay,
1280 rest gets virtualized.
1281 Now we have two linked triangles with one improper keeping them flat */
1282 if (atNR != nrfound)
1284 gmx_incons("Number of atom types in gen_vsites_tyr");
1287 /* Aromatic rings have 6-fold symmetry, so we only need one bond length
1288 * for the ring part (angle is always 120 degrees).
1290 bond_cc = get_ddb_bond(vsitetop, "TYR", "CD1", "CE1");
1291 bond_ch = get_ddb_bond(vsitetop, "TYR", "CD1", "HD1");
1292 bond_co = get_ddb_bond(vsitetop, "TYR", "CZ", "OH");
1293 bond_oh = get_ddb_bond(vsitetop, "TYR", "OH", "HH");
1294 angle_coh = DEG2RAD * get_ddb_angle(vsitetop, "TYR", "CZ", "OH", "HH");
1296 xi[atCG] = -bond_cc + bond_cc * std::cos(ANGLE_6RING);
1297 xi[atCD1] = -bond_cc;
1298 xi[atHD1] = xi[atCD1] + bond_ch * std::cos(ANGLE_6RING);
1300 xi[atHE1] = xi[atCE1] - bond_ch * std::cos(ANGLE_6RING);
1301 xi[atCD2] = xi[atCD1];
1302 xi[atHD2] = xi[atHD1];
1303 xi[atCE2] = xi[atCE1];
1304 xi[atHE2] = xi[atHE1];
1305 xi[atCZ] = bond_cc * std::cos(0.5 * ANGLE_6RING);
1306 xi[atOH] = xi[atCZ] + bond_co;
1309 for (i = 0; i < atOH; i++)
1311 xcom += xi[i] * at->atom[ats[i]].m;
1312 mtot += at->atom[ats[i]].m;
1316 /* first do 6 ring as default,
1317 except CZ (we'll do that different) and HZ (we don't have that): */
1318 nvsite = gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, FALSE);
1320 /* then construct CZ from the 2nd triangle */
1321 /* vsite3 construction: r_d = r_i + a r_ij + b r_ik */
1322 a = b = 0.5 * bond_co / (bond_co - bond_cc * std::cos(ANGLE_6RING));
1323 add_vsite3_param(&plist[F_VSITE3], ats[atCZ], ats[atOH], ats[atCE1], ats[atCE2], a, b);
1324 at->atom[ats[atCZ]].m = at->atom[ats[atCZ]].mB = 0;
1326 /* constraints between CE1, CE2 and OH */
1327 dCGCE = std::sqrt(cosrule(bond_cc, bond_cc, ANGLE_6RING));
1328 dCEOH = std::sqrt(cosrule(bond_cc, bond_co, ANGLE_6RING));
1329 my_add_param(&(plist[F_CONSTRNC]), ats[atCE1], ats[atOH], dCEOH);
1330 my_add_param(&(plist[F_CONSTRNC]), ats[atCE2], ats[atOH], dCEOH);
1332 /* We also want to constrain the angle C-O-H, but since CZ is constructed
1333 * we need to introduce a constraint to CG.
1334 * CG is much further away, so that will lead to instabilities in LINCS
1335 * when we constrain both CG-HH and OH-HH distances. Instead of requiring
1336 * the use of lincs_order=8 we introduce a dummy mass three times further
1337 * away from OH than HH. The mass is accordingly a third, with the remaining
1338 * 2/3 moved to OH. This shouldn't cause any problems since the forces will
1339 * apply to the HH constructed atom and not directly on the virtual mass.
1342 vdist = 2.0 * bond_oh;
1343 mM = at->atom[ats[atHH]].m / 2.0;
1344 at->atom[ats[atOH]].m += mM; /* add 1/2 of original H mass */
1345 at->atom[ats[atOH]].mB += mM; /* add 1/2 of original H mass */
1346 at->atom[ats[atHH]].m = at->atom[ats[atHH]].mB = 0;
1348 /* get dummy mass type */
1349 tpM = vsite_nm2type("MW", atype);
1350 /* make space for 1 mass: shift HH only */
1355 fprintf(stderr, "Inserting 1 dummy mass at %d\n", (*o2n)[i0] + 1);
1358 for (j = i0; j < at->nr; j++)
1360 (*o2n)[j] = j + *nadd;
1362 newx->resize(at->nr + *nadd);
1363 srenew(*newatom, at->nr + *nadd);
1364 srenew(*newatomname, at->nr + *nadd);
1365 srenew(*newvsite_type, at->nr + *nadd);
1366 srenew(*newcgnr, at->nr + *nadd);
1367 (*newatomname)[at->nr + *nadd - 1] = nullptr;
1369 /* Calc the dummy mass initial position */
1370 rvec_sub(x[ats[atHH]], x[ats[atOH]], r1);
1372 rvec_add(r1, x[ats[atHH]], (*newx)[atM]);
1374 strcpy(name, "MW1");
1375 (*newatomname)[atM] = put_symtab(symtab, name);
1376 (*newatom)[atM].m = (*newatom)[atM].mB = mM;
1377 (*newatom)[atM].q = (*newatom)[atM].qB = 0.0;
1378 (*newatom)[atM].type = (*newatom)[atM].typeB = tpM;
1379 (*newatom)[atM].ptype = eptAtom;
1380 (*newatom)[atM].resind = at->atom[i0].resind;
1381 (*newatom)[atM].elem[0] = 'M';
1382 (*newatom)[atM].elem[1] = '\0';
1383 (*newvsite_type)[atM] = NOTSET;
1384 (*newcgnr)[atM] = (*cgnr)[i0];
1385 /* renumber cgnr: */
1386 for (i = i0; i < at->nr; i++)
1391 (*vsite_type)[ats[atHH]] = F_VSITE2;
1393 /* assume we also want the COH angle constrained: */
1394 tmp1 = bond_cc * std::cos(0.5 * ANGLE_6RING) + dCGCE * std::sin(ANGLE_6RING * 0.5) + bond_co;
1395 dCGM = std::sqrt(cosrule(tmp1, vdist, angle_coh));
1396 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], add_shift + atM, dCGM);
1397 my_add_param(&(plist[F_CONSTRNC]), ats[atOH], add_shift + atM, vdist);
1399 add_vsite2_param(&plist[F_VSITE2], ats[atHH], ats[atOH], add_shift + atM, 1.0 / 2.0);
1403 static int gen_vsites_his(t_atoms* at,
1405 gmx::ArrayRef<InteractionsOfType> plist,
1408 gmx::ArrayRef<const VirtualSiteTopology> vsitetop)
1411 real a, b, alpha, dCGCE1, dCGNE2;
1412 real sinalpha, cosalpha;
1413 real xcom, ycom, mtot;
1414 real mG, mrest, mCE1, mNE2;
1415 real b_CG_ND1, b_ND1_CE1, b_CE1_NE2, b_CG_CD2, b_CD2_NE2;
1416 real b_ND1_HD1, b_NE2_HE2, b_CE1_HE1, b_CD2_HD2;
1417 real a_CG_ND1_CE1, a_CG_CD2_NE2, a_ND1_CE1_NE2, a_CE1_NE2_CD2;
1418 real a_NE2_CE1_HE1, a_NE2_CD2_HD2, a_CE1_ND1_HD1, a_CE1_NE2_HE2;
1421 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
1435 real x[atNR], y[atNR];
1437 /* CG, CE1 and NE2 stay, each gets part of the total mass,
1438 rest gets virtualized */
1439 /* check number of atoms, 3 hydrogens may be missing: */
1440 /* assert( nrfound >= atNR-3 || nrfound <= atNR );
1441 * Don't understand the above logic. Shouldn't it be && rather than || ???
1443 if ((nrfound < atNR - 3) || (nrfound > atNR))
1445 gmx_incons("Generating vsites for HIS");
1448 /* avoid warnings about uninitialized variables */
1449 b_ND1_HD1 = b_NE2_HE2 = b_CE1_HE1 = b_CD2_HD2 = a_NE2_CE1_HE1 = a_NE2_CD2_HD2 = a_CE1_ND1_HD1 =
1452 if (ats[atHD1] != NOTSET)
1454 if (ats[atHE2] != NOTSET)
1456 sprintf(resname, "HISH");
1460 sprintf(resname, "HISA");
1465 sprintf(resname, "HISB");
1468 /* Get geometry from database */
1469 b_CG_ND1 = get_ddb_bond(vsitetop, resname, "CG", "ND1");
1470 b_ND1_CE1 = get_ddb_bond(vsitetop, resname, "ND1", "CE1");
1471 b_CE1_NE2 = get_ddb_bond(vsitetop, resname, "CE1", "NE2");
1472 b_CG_CD2 = get_ddb_bond(vsitetop, resname, "CG", "CD2");
1473 b_CD2_NE2 = get_ddb_bond(vsitetop, resname, "CD2", "NE2");
1474 a_CG_ND1_CE1 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CG", "ND1", "CE1");
1475 a_CG_CD2_NE2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CG", "CD2", "NE2");
1476 a_ND1_CE1_NE2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "ND1", "CE1", "NE2");
1477 a_CE1_NE2_CD2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CE1", "NE2", "CD2");
1479 if (ats[atHD1] != NOTSET)
1481 b_ND1_HD1 = get_ddb_bond(vsitetop, resname, "ND1", "HD1");
1482 a_CE1_ND1_HD1 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CE1", "ND1", "HD1");
1484 if (ats[atHE2] != NOTSET)
1486 b_NE2_HE2 = get_ddb_bond(vsitetop, resname, "NE2", "HE2");
1487 a_CE1_NE2_HE2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CE1", "NE2", "HE2");
1489 if (ats[atHD2] != NOTSET)
1491 b_CD2_HD2 = get_ddb_bond(vsitetop, resname, "CD2", "HD2");
1492 a_NE2_CD2_HD2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "NE2", "CD2", "HD2");
1494 if (ats[atHE1] != NOTSET)
1496 b_CE1_HE1 = get_ddb_bond(vsitetop, resname, "CE1", "HE1");
1497 a_NE2_CE1_HE1 = DEG2RAD * get_ddb_angle(vsitetop, resname, "NE2", "CE1", "HE1");
1500 /* constraints between CG, CE1 and NE1 */
1501 dCGCE1 = std::sqrt(cosrule(b_CG_ND1, b_ND1_CE1, a_CG_ND1_CE1));
1502 dCGNE2 = std::sqrt(cosrule(b_CG_CD2, b_CD2_NE2, a_CG_CD2_NE2));
1504 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atCE1], dCGCE1);
1505 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atNE2], dCGNE2);
1506 /* we already have a constraint CE1-NE2, so we don't add it again */
1508 /* calculate the positions in a local frame of reference.
1509 * The x-axis is the line from CG that makes a right angle
1510 * with the bond CE1-NE2, and the y-axis the bond CE1-NE2.
1512 /* First calculate the x-axis intersection with y-axis (=yCE1).
1513 * Get cos(angle CG-CE1-NE2) :
1515 cosalpha = acosrule(dCGNE2, dCGCE1, b_CE1_NE2);
1517 y[atCE1] = cosalpha * dCGCE1;
1519 y[atNE2] = y[atCE1] - b_CE1_NE2;
1520 sinalpha = std::sqrt(1 - cosalpha * cosalpha);
1521 x[atCG] = -sinalpha * dCGCE1;
1523 x[atHE1] = x[atHE2] = x[atHD1] = x[atHD2] = 0;
1524 y[atHE1] = y[atHE2] = y[atHD1] = y[atHD2] = 0;
1526 /* calculate ND1 and CD2 positions from CE1 and NE2 */
1528 x[atND1] = -b_ND1_CE1 * std::sin(a_ND1_CE1_NE2);
1529 y[atND1] = y[atCE1] - b_ND1_CE1 * std::cos(a_ND1_CE1_NE2);
1531 x[atCD2] = -b_CD2_NE2 * std::sin(a_CE1_NE2_CD2);
1532 y[atCD2] = y[atNE2] + b_CD2_NE2 * std::cos(a_CE1_NE2_CD2);
1534 /* And finally the hydrogen positions */
1535 if (ats[atHE1] != NOTSET)
1537 x[atHE1] = x[atCE1] + b_CE1_HE1 * std::sin(a_NE2_CE1_HE1);
1538 y[atHE1] = y[atCE1] - b_CE1_HE1 * std::cos(a_NE2_CE1_HE1);
1540 /* HD2 - first get (ccw) angle from (positive) y-axis */
1541 if (ats[atHD2] != NOTSET)
1543 alpha = a_CE1_NE2_CD2 + M_PI - a_NE2_CD2_HD2;
1544 x[atHD2] = x[atCD2] - b_CD2_HD2 * std::sin(alpha);
1545 y[atHD2] = y[atCD2] + b_CD2_HD2 * std::cos(alpha);
1547 if (ats[atHD1] != NOTSET)
1549 /* HD1 - first get (cw) angle from (positive) y-axis */
1550 alpha = a_ND1_CE1_NE2 + M_PI - a_CE1_ND1_HD1;
1551 x[atHD1] = x[atND1] - b_ND1_HD1 * std::sin(alpha);
1552 y[atHD1] = y[atND1] - b_ND1_HD1 * std::cos(alpha);
1554 if (ats[atHE2] != NOTSET)
1556 x[atHE2] = x[atNE2] + b_NE2_HE2 * std::sin(a_CE1_NE2_HE2);
1557 y[atHE2] = y[atNE2] + b_NE2_HE2 * std::cos(a_CE1_NE2_HE2);
1559 /* Have all coordinates now */
1561 /* calc center-of-mass; keep atoms CG, CE1, NE2 and
1562 * set the rest to vsite3
1564 mtot = xcom = ycom = 0;
1566 for (i = 0; i < atNR; i++)
1568 if (ats[i] != NOTSET)
1570 mtot += at->atom[ats[i]].m;
1571 xcom += x[i] * at->atom[ats[i]].m;
1572 ycom += y[i] * at->atom[ats[i]].m;
1573 if (i != atCG && i != atCE1 && i != atNE2)
1575 at->atom[ats[i]].m = at->atom[ats[i]].mB = 0;
1576 (*vsite_type)[ats[i]] = F_VSITE3;
1581 if (nvsite + 3 != nrfound)
1583 gmx_incons("Generating vsites for HIS");
1589 /* distribute mass so that com stays the same */
1590 mG = xcom * mtot / x[atCG];
1592 mCE1 = (ycom - y[atNE2]) * mrest / (y[atCE1] - y[atNE2]);
1593 mNE2 = mrest - mCE1;
1595 at->atom[ats[atCG]].m = at->atom[ats[atCG]].mB = mG;
1596 at->atom[ats[atCE1]].m = at->atom[ats[atCE1]].mB = mCE1;
1597 at->atom[ats[atNE2]].m = at->atom[ats[atNE2]].mB = mNE2;
1600 if (ats[atHE1] != NOTSET)
1603 x[atHE1], y[atHE1], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG], &a, &b);
1604 add_vsite3_param(&plist[F_VSITE3], ats[atHE1], ats[atCE1], ats[atNE2], ats[atCG], a, b);
1607 if (ats[atHE2] != NOTSET)
1610 x[atHE2], y[atHE2], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG], &a, &b);
1611 add_vsite3_param(&plist[F_VSITE3], ats[atHE2], ats[atNE2], ats[atCE1], ats[atCG], a, b);
1616 x[atND1], y[atND1], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG], &a, &b);
1617 add_vsite3_param(&plist[F_VSITE3], ats[atND1], ats[atNE2], ats[atCE1], ats[atCG], a, b);
1621 x[atCD2], y[atCD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG], &a, &b);
1622 add_vsite3_param(&plist[F_VSITE3], ats[atCD2], ats[atCE1], ats[atNE2], ats[atCG], a, b);
1625 if (ats[atHD1] != NOTSET)
1628 x[atHD1], y[atHD1], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG], &a, &b);
1629 add_vsite3_param(&plist[F_VSITE3], ats[atHD1], ats[atNE2], ats[atCE1], ats[atCG], a, b);
1632 if (ats[atHD2] != NOTSET)
1635 x[atHD2], y[atHD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG], &a, &b);
1636 add_vsite3_param(&plist[F_VSITE3], ats[atHD2], ats[atCE1], ats[atNE2], ats[atCG], a, b);
1641 static bool is_vsite(int vsite_type)
1643 if (vsite_type == NOTSET)
1647 switch (abs(vsite_type))
1654 case F_VSITE4FDN: return TRUE;
1655 default: return FALSE;
1659 static char atomnamesuffix[] = "1234";
1661 void do_vsites(gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
1662 PreprocessingAtomTypes* atype,
1665 std::vector<gmx::RVec>* x,
1666 gmx::ArrayRef<InteractionsOfType> plist,
1670 bool bVsiteAromatics,
1673 #define MAXATOMSPERRESIDUE 16
1674 int k, m, i0, ni0, whatres, add_shift, nvsite, nadd;
1676 int nrfound = 0, needed, nrbonds, nrHatoms, Heavy, nrheavies, tpM, tpHeavy;
1677 int Hatoms[4], heavies[4];
1678 bool bWARNING, bAddVsiteParam, bFirstWater;
1680 real mHtot, mtot, fact, fact2;
1681 rvec rpar, rperp, temp;
1682 char tpname[32], nexttpname[32];
1683 int * o2n, *newvsite_type, *newcgnr, ats[MAXATOMSPERRESIDUE];
1685 char*** newatomname;
1687 bool isN, planarN, bFound;
1689 /* if bVsiteAromatics=TRUE do_vsites will specifically convert atoms in
1690 PHE, TRP, TYR and HIS to a construction of virtual sites */
1699 const char* resnms[resNR] = { "PHE", "TRP", "TYR", "HIS" };
1700 /* Amber03 alternative names for termini */
1701 const char* resnmsN[resNR] = { "NPHE", "NTRP", "NTYR", "NHIS" };
1702 const char* resnmsC[resNR] = { "CPHE", "CTRP", "CTYR", "CHIS" };
1703 /* HIS can be known as HISH, HIS1, HISA, HID, HIE, HIP, etc. too */
1704 bool bPartial[resNR] = { FALSE, FALSE, FALSE, TRUE };
1705 /* the atnms for every residue MUST correspond to the enums in the
1706 gen_vsites_* (one for each residue) routines! */
1707 /* also the atom names in atnms MUST be in the same order as in the .rtp! */
1708 const char* atnms[resNR][MAXATOMSPERRESIDUE + 1] = { { "CG", /* PHE */
1763 printf("Searching for atoms to make virtual sites ...\n");
1764 fprintf(debug, "# # # VSITES # # #\n");
1767 std::vector<std::string> db = fflib_search_file_end(ffdir, ".vsd", FALSE);
1769 /* Container of CH3/NH3/NH2 configuration entries.
1770 * See comments in read_vsite_database. It isnt beautiful,
1771 * but it had to be fixed, and I dont even want to try to
1772 * maintain this part of the code...
1774 std::vector<VirtualSiteConfiguration> vsiteconflist;
1776 // TODO those have been deprecated and should be removed completely.
1777 /* Container of geometry (bond/angle) entries for
1778 * residues like PHE, TRP, TYR, HIS, etc., where we need
1779 * to know the geometry to construct vsite aromatics.
1780 * Note that equilibrium geometry isnt necessarily the same
1781 * as the individual bond and angle values given in the
1782 * force field (rings can be strained).
1784 std::vector<VirtualSiteTopology> vsitetop;
1785 for (const auto& filename : db)
1787 read_vsite_database(filename.c_str(), &vsiteconflist, &vsitetop);
1793 /* we need a marker for which atoms should *not* be renumbered afterwards */
1794 add_shift = 10 * at->nr;
1795 /* make arrays where masses can be inserted into */
1796 std::vector<gmx::RVec> newx(at->nr);
1797 snew(newatom, at->nr);
1798 snew(newatomname, at->nr);
1799 snew(newvsite_type, at->nr);
1800 snew(newcgnr, at->nr);
1801 /* make index array to tell where the atoms go to when masses are inserted */
1803 for (int i = 0; i < at->nr; i++)
1807 /* make index to tell which residues were already processed */
1808 std::vector<bool> bResProcessed(at->nres);
1812 /* generate vsite constructions */
1813 /* loop over all atoms */
1815 for (int i = 0; (i < at->nr); i++)
1817 if (at->atom[i].resind != resind)
1819 resind = at->atom[i].resind;
1821 const char* resnm = *(at->resinfo[resind].name);
1822 /* first check for aromatics to virtualize */
1823 /* don't waste our effort on DNA, water etc. */
1824 /* Only do the vsite aromatic stuff when we reach the
1825 * CA atom, since there might be an X2/X3 group on the
1826 * N-terminus that must be treated first.
1828 if (bVsiteAromatics && (strcmp(*(at->atomname[i]), "CA") == 0) && !bResProcessed[resind]
1829 && rt.namedResidueHasType(*(at->resinfo[resind].name), "Protein"))
1831 /* mark this residue */
1832 bResProcessed[resind] = TRUE;
1833 /* find out if this residue needs converting */
1835 for (int j = 0; j < resNR && whatres == NOTSET; j++)
1838 cmplength = bPartial[j] ? strlen(resnm) - 1 : strlen(resnm);
1840 bFound = ((gmx::equalCaseInsensitive(resnm, resnms[j], cmplength))
1841 || (gmx::equalCaseInsensitive(resnm, resnmsN[j], cmplength))
1842 || (gmx::equalCaseInsensitive(resnm, resnmsC[j], cmplength)));
1847 /* get atoms we will be needing for the conversion */
1849 for (k = 0; atnms[j][k]; k++)
1852 for (m = i; m < at->nr && at->atom[m].resind == resind && ats[k] == NOTSET; m++)
1854 if (gmx_strcasecmp(*(at->atomname[m]), atnms[j][k]) == 0)
1862 /* now k is number of atom names in atnms[j] */
1871 if (nrfound < needed)
1874 "not enough atoms found (%d, need %d) in "
1875 "residue %s %d while\n "
1876 "generating aromatics virtual site construction",
1880 at->resinfo[resind].nr);
1882 /* Advance overall atom counter */
1886 /* the enums for every residue MUST correspond to atnms[residue] */
1892 fprintf(stderr, "PHE at %d\n", o2n[ats[0]] + 1);
1894 nvsite += gen_vsites_phe(at, vsite_type, plist, nrfound, ats, vsitetop);
1899 fprintf(stderr, "TRP at %d\n", o2n[ats[0]] + 1);
1901 nvsite += gen_vsites_trp(atype,
1923 fprintf(stderr, "TYR at %d\n", o2n[ats[0]] + 1);
1925 nvsite += gen_vsites_tyr(atype,
1947 fprintf(stderr, "HIS at %d\n", o2n[ats[0]] + 1);
1949 nvsite += gen_vsites_his(at, vsite_type, plist, nrfound, ats, vsitetop);
1952 /* this means this residue won't be processed */
1954 default: gmx_fatal(FARGS, "DEATH HORROR in do_vsites (%s:%d)", __FILE__, __LINE__);
1955 } /* switch whatres */
1956 /* skip back to beginning of residue */
1957 while (i > 0 && at->atom[i - 1].resind == resind)
1961 } /* if bVsiteAromatics & is protein */
1963 /* now process the rest of the hydrogens */
1964 /* only process hydrogen atoms which are not already set */
1965 if (((*vsite_type)[i] == NOTSET) && is_hydrogen(*(at->atomname[i])))
1967 /* find heavy atom, count #bonds from it and #H atoms bound to it
1968 and return H atom numbers (Hatoms) and heavy atom numbers (heavies) */
1969 count_bonds(i, &plist[F_BONDS], at->atomname, &nrbonds, &nrHatoms, Hatoms, &Heavy, &nrheavies, heavies);
1970 /* get Heavy atom type */
1971 tpHeavy = get_atype(Heavy, at, rtpFFDB, &rt);
1972 strcpy(tpname, *atype->atomNameFromAtomType(tpHeavy));
1975 bAddVsiteParam = TRUE;
1976 /* nested if's which check nrHatoms, nrbonds and atomname */
1981 case 2: /* -O-H */ (*vsite_type)[i] = F_BONDS; break;
1982 case 3: /* =CH-, -NH- or =NH+- */ (*vsite_type)[i] = F_VSITE3FD; break;
1983 case 4: /* --CH- (tert) */
1984 /* The old type 4FD had stability issues, so
1985 * all new constructs should use 4FDN
1987 (*vsite_type)[i] = F_VSITE4FDN;
1989 /* Check parity of heavy atoms from coordinates */
1994 rvec_sub((*x)[aj], (*x)[ai], tmpmat[0]);
1995 rvec_sub((*x)[ak], (*x)[ai], tmpmat[1]);
1996 rvec_sub((*x)[al], (*x)[ai], tmpmat[2]);
1998 if (det(tmpmat) > 0)
2006 default: /* nrbonds != 2, 3 or 4 */ bWARNING = TRUE;
2009 else if ((nrHatoms == 2) && (nrbonds == 2) && (at->atom[Heavy].atomnumber == 8))
2011 bAddVsiteParam = FALSE; /* this is water: skip these hydrogens */
2014 bFirstWater = FALSE;
2017 fprintf(debug, "Not converting hydrogens in water to virtual sites\n");
2021 else if ((nrHatoms == 2) && (nrbonds == 4))
2023 /* -CH2- , -NH2+- */
2024 (*vsite_type)[Hatoms[0]] = F_VSITE3OUT;
2025 (*vsite_type)[Hatoms[1]] = -F_VSITE3OUT;
2029 /* 2 or 3 hydrogen atom, with 3 or 4 bonds in total to the heavy atom.
2030 * If it is a nitrogen, first check if it is planar.
2032 isN = planarN = FALSE;
2033 if ((nrHatoms == 2) && ((*at->atomname[Heavy])[0] == 'N'))
2036 int j = nitrogen_is_planar(vsiteconflist, tpname);
2039 gmx_fatal(FARGS, "No vsite database NH2 entry for type %s\n", tpname);
2043 if ((nrHatoms == 2) && (nrbonds == 3) && (!isN || planarN))
2045 /* =CH2 or, if it is a nitrogen NH2, it is a planar one */
2046 (*vsite_type)[Hatoms[0]] = F_VSITE3FAD;
2047 (*vsite_type)[Hatoms[1]] = -F_VSITE3FAD;
2049 else if (((nrHatoms == 2) && (nrbonds == 3) && (isN && !planarN))
2050 || ((nrHatoms == 3) && (nrbonds == 4)))
2052 /* CH3, NH3 or non-planar NH2 group */
2053 int Hat_vsite_type[3] = { F_VSITE3, F_VSITE3OUT, F_VSITE3OUT };
2054 bool Hat_SwapParity[3] = { FALSE, TRUE, FALSE };
2058 fprintf(stderr, "-XH3 or nonplanar NH2 group at %d\n", i + 1);
2060 bAddVsiteParam = FALSE; /* we'll do this ourselves! */
2061 /* -NH2 (umbrella), -NH3+ or -CH3 */
2062 (*vsite_type)[Heavy] = F_VSITE3;
2063 for (int j = 0; j < nrHatoms; j++)
2065 (*vsite_type)[Hatoms[j]] = Hat_vsite_type[j];
2067 /* get dummy mass type from first char of heavy atom type (N or C) */
2070 *atype->atomNameFromAtomType(get_atype(heavies[0], at, rtpFFDB, &rt)));
2071 std::string ch = get_dummymass_name(vsiteconflist, tpname, nexttpname);
2079 "Can't find dummy mass for type %s bonded to type %s in the "
2080 "virtual site database (.vsd files). Add it to the database!\n",
2087 "A dummy mass for type %s bonded to type %s is required, but "
2088 "no virtual site database (.vsd) files where found.\n",
2098 tpM = vsite_nm2type(name.c_str(), atype);
2099 /* make space for 2 masses: shift all atoms starting with 'Heavy' */
2105 fprintf(stderr, "Inserting %d dummy masses at %d\n", NMASS, o2n[i0] + 1);
2108 for (int j = i0; j < at->nr; j++)
2113 newx.resize(at->nr + nadd);
2114 srenew(newatom, at->nr + nadd);
2115 srenew(newatomname, at->nr + nadd);
2116 srenew(newvsite_type, at->nr + nadd);
2117 srenew(newcgnr, at->nr + nadd);
2119 for (int j = 0; j < NMASS; j++)
2121 newatomname[at->nr + nadd - 1 - j] = nullptr;
2124 /* calculate starting position for the masses */
2126 /* get atom masses, and set Heavy and Hatoms mass to zero */
2127 for (int j = 0; j < nrHatoms; j++)
2129 mHtot += get_amass(Hatoms[j], at, rtpFFDB, &rt);
2130 at->atom[Hatoms[j]].m = at->atom[Hatoms[j]].mB = 0;
2132 mtot = mHtot + get_amass(Heavy, at, rtpFFDB, &rt);
2133 at->atom[Heavy].m = at->atom[Heavy].mB = 0;
2138 fact2 = mHtot / mtot;
2139 fact = std::sqrt(fact2);
2140 /* generate vectors parallel and perpendicular to rotational axis:
2141 * rpar = Heavy -> Hcom
2142 * rperp = Hcom -> H1 */
2144 for (int j = 0; j < nrHatoms; j++)
2146 rvec_inc(rpar, (*x)[Hatoms[j]]);
2148 svmul(1.0 / nrHatoms, rpar, rpar); /* rpar = ( H1+H2+H3 ) / 3 */
2149 rvec_dec(rpar, (*x)[Heavy]); /* - Heavy */
2150 rvec_sub((*x)[Hatoms[0]], (*x)[Heavy], rperp);
2151 rvec_dec(rperp, rpar); /* rperp = H1 - Heavy - rpar */
2152 /* calc mass positions */
2153 svmul(fact2, rpar, temp);
2154 for (int j = 0; (j < NMASS); j++) /* xM = xN + fact2 * rpar +/- fact * rperp */
2156 rvec_add((*x)[Heavy], temp, newx[ni0 + j]);
2158 svmul(fact, rperp, temp);
2159 rvec_inc(newx[ni0], temp);
2160 rvec_dec(newx[ni0 + 1], temp);
2161 /* set atom parameters for the masses */
2162 for (int j = 0; (j < NMASS); j++)
2164 /* make name: "M??#" or "M?#" (? is atomname, # is number) */
2167 for (k = 0; (*at->atomname[Heavy])[k] && (k < NMASS); k++)
2169 name[k + 1] = (*at->atomname[Heavy])[k];
2171 name[k + 1] = atomnamesuffix[j];
2173 newatomname[ni0 + j] = put_symtab(symtab, name.c_str());
2174 newatom[ni0 + j].m = newatom[ni0 + j].mB = mtot / NMASS;
2175 newatom[ni0 + j].q = newatom[ni0 + j].qB = 0.0;
2176 newatom[ni0 + j].type = newatom[ni0 + j].typeB = tpM;
2177 newatom[ni0 + j].ptype = eptAtom;
2178 newatom[ni0 + j].resind = at->atom[i0].resind;
2179 newatom[ni0 + j].elem[0] = 'M';
2180 newatom[ni0 + j].elem[1] = '\0';
2181 newvsite_type[ni0 + j] = NOTSET;
2182 newcgnr[ni0 + j] = (*cgnr)[i0];
2184 /* add constraints between dummy masses and to heavies[0] */
2185 /* 'add_shift' says which atoms won't be renumbered afterwards */
2186 my_add_param(&(plist[F_CONSTRNC]), heavies[0], add_shift + ni0, NOTSET);
2187 my_add_param(&(plist[F_CONSTRNC]), heavies[0], add_shift + ni0 + 1, NOTSET);
2188 my_add_param(&(plist[F_CONSTRNC]), add_shift + ni0, add_shift + ni0 + 1, NOTSET);
2190 /* generate Heavy, H1, H2 and H3 from M1, M2 and heavies[0] */
2191 /* note that vsite_type cannot be NOTSET, because we just set it */
2192 add_vsite3_atoms(&plist[(*vsite_type)[Heavy]],
2196 add_shift + ni0 + 1,
2198 for (int j = 0; j < nrHatoms; j++)
2200 add_vsite3_atoms(&plist[(*vsite_type)[Hatoms[j]]],
2204 add_shift + ni0 + 1,
2217 "Cannot convert atom %d %s (bound to a heavy atom "
2219 " %d bonds and %d bound hydrogens atoms) to virtual site\n",
2228 /* add vsite parameters to topology,
2229 also get rid of negative vsite_types */
2230 add_vsites(plist, (*vsite_type), Heavy, nrHatoms, Hatoms, nrheavies, heavies);
2231 /* transfer mass of virtual site to Heavy atom */
2232 for (int j = 0; j < nrHatoms; j++)
2234 if (is_vsite((*vsite_type)[Hatoms[j]]))
2236 at->atom[Heavy].m += at->atom[Hatoms[j]].m;
2237 at->atom[Heavy].mB = at->atom[Heavy].m;
2238 at->atom[Hatoms[j]].m = at->atom[Hatoms[j]].mB = 0;
2245 fprintf(debug, "atom %d: ", o2n[i] + 1);
2246 print_bonds(debug, o2n, nrHatoms, Hatoms, Heavy, nrheavies, heavies);
2248 } /* if vsite NOTSET & is hydrogen */
2250 } /* for i < at->nr */
2254 fprintf(debug, "Before inserting new atoms:\n");
2255 for (int i = 0; i < at->nr; i++)
2258 "%4d %4d %4s %4d %4s %6d %-10s\n",
2261 at->atomname[i] ? *(at->atomname[i]) : "(NULL)",
2262 at->resinfo[at->atom[i].resind].nr,
2263 at->resinfo[at->atom[i].resind].name ? *(at->resinfo[at->atom[i].resind].name) : "(NULL)",
2265 ((*vsite_type)[i] == NOTSET) ? "NOTSET" : interaction_function[(*vsite_type)[i]].name);
2267 fprintf(debug, "new atoms to be inserted:\n");
2268 for (int i = 0; i < at->nr + nadd; i++)
2273 "%4d %4s %4d %6d %-10s\n",
2275 newatomname[i] ? *(newatomname[i]) : "(NULL)",
2278 (newvsite_type[i] == NOTSET) ? "NOTSET"
2279 : interaction_function[newvsite_type[i]].name);
2284 /* add all original atoms to the new arrays, using o2n index array */
2285 for (int i = 0; i < at->nr; i++)
2287 newatomname[o2n[i]] = at->atomname[i];
2288 newatom[o2n[i]] = at->atom[i];
2289 newvsite_type[o2n[i]] = (*vsite_type)[i];
2290 newcgnr[o2n[i]] = (*cgnr)[i];
2291 copy_rvec((*x)[i], newx[o2n[i]]);
2293 /* throw away old atoms */
2295 sfree(at->atomname);
2298 /* put in the new ones */
2301 at->atomname = newatomname;
2302 *vsite_type = newvsite_type;
2305 if (at->nr > add_shift)
2308 "Added impossible amount of dummy masses "
2309 "(%d on a total of %d atoms)\n",
2316 fprintf(debug, "After inserting new atoms:\n");
2317 for (int i = 0; i < at->nr; i++)
2320 "%4d %4s %4d %4s %6d %-10s\n",
2322 at->atomname[i] ? *(at->atomname[i]) : "(NULL)",
2323 at->resinfo[at->atom[i].resind].nr,
2324 at->resinfo[at->atom[i].resind].name ? *(at->resinfo[at->atom[i].resind].name) : "(NULL)",
2326 ((*vsite_type)[i] == NOTSET) ? "NOTSET" : interaction_function[(*vsite_type)[i]].name);
2330 /* now renumber all the interactions because of the added atoms */
2331 for (int ftype = 0; ftype < F_NRE; ftype++)
2333 InteractionsOfType* params = &(plist[ftype]);
2336 fprintf(debug, "Renumbering %zu %s\n", params->size(), interaction_function[ftype].longname);
2338 /* Horrible hacks needed here to get this to work */
2339 for (auto parm = params->interactionTypes.begin(); parm != params->interactionTypes.end(); parm++)
2341 gmx::ArrayRef<const int> atomNumbers(parm->atoms());
2342 std::vector<int> newAtomNumber;
2343 for (int j = 0; j < NRAL(ftype); j++)
2345 if (atomNumbers[j] >= add_shift)
2349 fprintf(debug, " [%d -> %d]", atomNumbers[j], atomNumbers[j] - add_shift);
2351 newAtomNumber.emplace_back(atomNumbers[j] - add_shift);
2357 fprintf(debug, " [%d -> %d]", atomNumbers[j], o2n[atomNumbers[j]]);
2359 newAtomNumber.emplace_back(o2n[atomNumbers[j]]);
2362 *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
2365 fprintf(debug, "\n");
2369 /* sort constraint parameters */
2370 InteractionsOfType* params = &(plist[F_CONSTRNC]);
2371 for (auto& type : params->interactionTypes)
2379 /* tell the user what we did */
2380 fprintf(stderr, "Marked %d virtual sites\n", nvsite);
2381 fprintf(stderr, "Added %d dummy masses\n", nadd);
2382 fprintf(stderr, "Added %zu new constraints\n", plist[F_CONSTRNC].size());
2385 void do_h_mass(InteractionsOfType* psb, int vsite_type[], t_atoms* at, real mHmult, bool bDeuterate)
2387 /* loop over all atoms */
2388 for (int i = 0; i < at->nr; i++)
2390 /* adjust masses if i is hydrogen and not a virtual site */
2391 if (!is_vsite(vsite_type[i]) && is_hydrogen(*(at->atomname[i])))
2393 /* find bonded heavy atom */
2395 for (auto parm = psb->interactionTypes.begin();
2396 (parm != psb->interactionTypes.end()) && (a == NOTSET);
2399 /* if other atom is not a virtual site, it is the one we want */
2400 if ((parm->ai() == i) && !is_vsite(vsite_type[parm->aj()]))
2404 else if ((parm->aj() == i) && !is_vsite(vsite_type[parm->ai()]))
2411 gmx_fatal(FARGS, "Unbound hydrogen atom (%d) found while adjusting mass", i + 1);
2414 /* adjust mass of i (hydrogen) with mHmult
2415 and correct mass of a (bonded atom) with same amount */
2418 at->atom[a].m -= (mHmult - 1.0) * at->atom[i].m;
2419 at->atom[a].mB -= (mHmult - 1.0) * at->atom[i].m;
2421 at->atom[i].m *= mHmult;
2422 at->atom[i].mB *= mHmult;