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46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/commandline/viewit.h"
48 #include "gromacs/fileio/confio.h"
49 #include "gromacs/fileio/trxio.h"
50 #include "gromacs/fileio/xvgr.h"
51 #include "gromacs/gmxana/gmx_ana.h"
52 #include "gromacs/math/functions.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/mdtypes/md_enums.h"
55 #include "gromacs/pbcutil/pbc.h"
56 #include "gromacs/pbcutil/rmpbc.h"
57 #include "gromacs/topology/index.h"
58 #include "gromacs/topology/topology.h"
59 #include "gromacs/utility/arraysize.h"
60 #include "gromacs/utility/cstringutil.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/futil.h"
63 #include "gromacs/utility/gmxassert.h"
64 #include "gromacs/utility/smalloc.h"
67 static void periodic_dist(int ePBC
, matrix box
, rvec x
[], int n
, const int index
[], real
* rmin
, real
* rmax
, int* min_ind
)
70 int nsz
, nshift
, sx
, sy
, sz
, i
, j
, s
;
71 real sqr_box
, r2min
, r2max
, r2
;
72 rvec shift
[NSHIFT_MAX
], d0
, d
;
74 sqr_box
= std::min(norm2(box
[XX
]), norm2(box
[YY
]));
77 sqr_box
= std::min(sqr_box
, norm2(box
[ZZ
]));
80 else if (ePBC
== epbcXY
)
86 gmx_fatal(FARGS
, "pbc = %s is not supported by g_mindist", epbc_names
[ePBC
]);
90 for (sz
= -nsz
; sz
<= nsz
; sz
++)
92 for (sy
= -1; sy
<= 1; sy
++)
94 for (sx
= -1; sx
<= 1; sx
++)
96 if (sx
!= 0 || sy
!= 0 || sz
!= 0)
98 for (i
= 0; i
< DIM
; i
++)
100 shift
[nshift
][i
] = sx
* box
[XX
][i
] + sy
* box
[YY
][i
] + sz
* box
[ZZ
][i
];
111 for (i
= 0; i
< n
; i
++)
113 for (j
= i
+ 1; j
< n
; j
++)
115 rvec_sub(x
[index
[i
]], x
[index
[j
]], d0
);
121 for (s
= 0; s
< nshift
; s
++)
123 rvec_add(d0
, shift
[s
], d
);
135 *rmin
= std::sqrt(r2min
);
136 *rmax
= std::sqrt(r2max
);
139 static void periodic_mindist_plot(const char* trxfn
,
141 const t_topology
* top
,
146 const gmx_output_env_t
* oenv
)
149 const char* leg
[5] = { "min per.", "max int.", "box1", "box2", "box3" };
154 int natoms
, ind_min
[2] = { 0, 0 }, ind_mini
= 0, ind_minj
= 0;
155 real rmin
, rmax
, rmint
, tmint
;
157 gmx_rmpbc_t gpbc
= nullptr;
159 natoms
= read_first_x(oenv
, &status
, trxfn
, &t
, &x
, box
);
161 check_index(nullptr, n
, index
, nullptr, natoms
);
163 out
= xvgropen(outfn
, "Minimum distance to periodic image", output_env_get_time_label(oenv
),
164 "Distance (nm)", oenv
);
165 if (output_env_get_print_xvgr_codes(oenv
))
167 fprintf(out
, "@ subtitle \"and maximum internal distance\"\n");
169 xvgr_legend(out
, 5, leg
, oenv
);
176 gpbc
= gmx_rmpbc_init(&top
->idef
, ePBC
, natoms
);
184 gmx_rmpbc(gpbc
, natoms
, box
, x
);
187 periodic_dist(ePBC
, box
, x
, n
, index
, &rmin
, &rmax
, ind_min
);
192 ind_mini
= ind_min
[0];
193 ind_minj
= ind_min
[1];
195 if (bSplit
&& !bFirst
&& std::abs(t
/ output_env_get_time_factor(oenv
)) < 1e-5)
197 fprintf(out
, "%s\n", output_env_get_print_xvgr_codes(oenv
) ? "&" : "");
199 fprintf(out
, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n", output_env_conv_time(oenv
, t
), rmin
,
200 rmax
, norm(box
[0]), norm(box
[1]), norm(box
[2]));
202 } while (read_next_x(oenv
, status
, &t
, x
, box
));
206 gmx_rmpbc_done(gpbc
);
212 "\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
213 "between atoms %d and %d\n",
214 rmint
, output_env_conv_time(oenv
, tmint
), output_env_get_time_unit(oenv
).c_str(),
215 index
[ind_mini
] + 1, index
[ind_minj
] + 1);
218 static void calc_dist(real rcut
,
237 int i
, j
, i0
= 0, j1
;
241 real r2
, rmin2
, rmax2
, rcut2
;
252 rcut2
= gmx::square(rcut
);
254 /* Must init pbc every step because of pressure coupling */
257 set_pbc(&pbc
, ePBC
, box
);
270 GMX_RELEASE_ASSERT(index1
!= nullptr, "Need a valid index for plotting distances");
275 for (j
= 0; (j
< j1
); j
++)
278 if (index2
== nullptr)
284 for (i
= i0
; (i
< nx1
); i
++)
291 pbc_dx(&pbc
, x
[ix
], x
[jx
], dx
);
295 rvec_sub(x
[ix
], x
[jx
], dx
);
337 *rmin
= std::sqrt(rmin2
);
338 *rmax
= std::sqrt(rmax2
);
341 static void dist_plot(const char* fn
,
349 const t_atoms
* atoms
,
361 gmx_bool bEachResEachTime
,
362 gmx_bool bPrintResName
,
363 const gmx_output_env_t
* oenv
)
365 FILE * atm
, *dist
, *num
;
369 real t
, dmin
, dmax
, **mindres
= nullptr, **maxdres
= nullptr;
373 int min2
, max2
, min1r
, min2r
, max1r
, max2r
;
380 FILE* respertime
= nullptr;
382 if (read_first_x(oenv
, &status
, fn
, &t
, &x0
, box
) == 0)
384 gmx_fatal(FARGS
, "Could not read coordinates from statusfile\n");
387 sprintf(buf
, "%simum Distance", bMin
? "Min" : "Max");
388 dist
= xvgropen(dfile
, buf
, output_env_get_time_label(oenv
), "Distance (nm)", oenv
);
389 sprintf(buf
, "Number of Contacts %s %g nm", bMin
? "<" : ">", rcut
);
390 num
= nfile
? xvgropen(nfile
, buf
, output_env_get_time_label(oenv
), "Number", oenv
) : nullptr;
391 atm
= afile
? gmx_ffopen(afile
, "w") : nullptr;
392 trxout
= xfile
? open_trx(xfile
, "w") : nullptr;
399 sprintf(buf
, "Internal in %s", grpn
[0]);
400 leg
[0] = gmx_strdup(buf
);
401 xvgr_legend(dist
, 0, leg
, oenv
);
404 xvgr_legend(num
, 0, leg
, oenv
);
409 GMX_RELEASE_ASSERT(ng
> 1, "Must have more than one group with bMat");
410 snew(leg
, (ng
* (ng
- 1)) / 2);
411 for (i
= j
= 0; (i
< ng
- 1); i
++)
413 for (k
= i
+ 1; (k
< ng
); k
++, j
++)
415 sprintf(buf
, "%s-%s", grpn
[i
], grpn
[k
]);
416 leg
[j
] = gmx_strdup(buf
);
419 xvgr_legend(dist
, j
, leg
, oenv
);
422 xvgr_legend(num
, j
, leg
, oenv
);
429 for (i
= 0; (i
< ng
- 1); i
++)
431 sprintf(buf
, "%s-%s", grpn
[0], grpn
[i
+ 1]);
432 leg
[i
] = gmx_strdup(buf
);
434 xvgr_legend(dist
, ng
- 1, leg
, oenv
);
437 xvgr_legend(num
, ng
- 1, leg
, oenv
);
441 if (bEachResEachTime
)
443 sprintf(buf
, "%simum Distance", bMin
? "Min" : "Max");
444 respertime
= xvgropen(rfile
, buf
, output_env_get_time_label(oenv
), "Distance (nm)", oenv
);
445 xvgr_legend(respertime
, ng
- 1, leg
, oenv
);
446 if (bPrintResName
&& output_env_get_print_xvgr_codes(oenv
))
448 fprintf(respertime
, "# ");
450 for (j
= 0; j
< nres
; j
++)
452 fprintf(respertime
, "%s%d ",
453 *(atoms
->resinfo
[atoms
->atom
[index
[0][residue
[j
]]].resind
].name
),
454 atoms
->atom
[index
[0][residue
[j
]]].resind
);
456 fprintf(respertime
, "\n");
462 snew(mindres
, ng
- 1);
463 snew(maxdres
, ng
- 1);
464 for (i
= 1; i
< ng
; i
++)
466 snew(mindres
[i
- 1], nres
);
467 snew(maxdres
[i
- 1], nres
);
468 for (j
= 0; j
< nres
; j
++)
470 mindres
[i
- 1][j
] = 1e6
;
472 /* maxdres[*][*] is already 0 */
478 if (bSplit
&& !bFirst
&& std::abs(t
/ output_env_get_time_factor(oenv
)) < 1e-5)
480 fprintf(dist
, "%s\n", output_env_get_print_xvgr_codes(oenv
) ? "&" : "");
483 fprintf(num
, "%s\n", output_env_get_print_xvgr_codes(oenv
) ? "&" : "");
487 fprintf(atm
, "%s\n", output_env_get_print_xvgr_codes(oenv
) ? "&" : "");
490 fprintf(dist
, "%12e", output_env_conv_time(oenv
, t
));
493 fprintf(num
, "%12e", output_env_conv_time(oenv
, t
));
500 calc_dist(rcut
, bPBC
, ePBC
, box
, x0
, gnx
[0], gnx
[0], index
[0], index
[0], bGroup
,
501 &dmin
, &dmax
, &nmin
, &nmax
, &min1
, &min2
, &max1
, &max2
);
502 fprintf(dist
, " %12e", bMin
? dmin
: dmax
);
505 fprintf(num
, " %8d", bMin
? nmin
: nmax
);
510 for (i
= 0; (i
< ng
- 1); i
++)
512 for (k
= i
+ 1; (k
< ng
); k
++)
514 calc_dist(rcut
, bPBC
, ePBC
, box
, x0
, gnx
[i
], gnx
[k
], index
[i
], index
[k
],
515 bGroup
, &dmin
, &dmax
, &nmin
, &nmax
, &min1
, &min2
, &max1
, &max2
);
516 fprintf(dist
, " %12e", bMin
? dmin
: dmax
);
519 fprintf(num
, " %8d", bMin
? nmin
: nmax
);
527 GMX_RELEASE_ASSERT(ng
> 1, "Must have more than one group when not using -matrix");
528 for (i
= 1; (i
< ng
); i
++)
530 calc_dist(rcut
, bPBC
, ePBC
, box
, x0
, gnx
[0], gnx
[i
], index
[0], index
[i
], bGroup
,
531 &dmin
, &dmax
, &nmin
, &nmax
, &min1
, &min2
, &max1
, &max2
);
532 fprintf(dist
, " %12e", bMin
? dmin
: dmax
);
535 fprintf(num
, " %8d", bMin
? nmin
: nmax
);
539 for (j
= 0; j
< nres
; j
++)
541 calc_dist(rcut
, bPBC
, ePBC
, box
, x0
, residue
[j
+ 1] - residue
[j
], gnx
[i
],
542 &(index
[0][residue
[j
]]), index
[i
], bGroup
, &dmin
, &dmax
, &nmin
,
543 &nmax
, &min1r
, &min2r
, &max1r
, &max2r
);
544 mindres
[i
- 1][j
] = std::min(mindres
[i
- 1][j
], dmin
);
545 maxdres
[i
- 1][j
] = std::max(maxdres
[i
- 1][j
], dmax
);
555 if ((bMin
? min1
: max1
) != -1)
559 fprintf(atm
, "%12e %12d %12d\n", output_env_conv_time(oenv
, t
),
560 1 + (bMin
? min1
: max1
), 1 + (bMin
? min2
: max2
));
566 oindex
[0] = bMin
? min1
: max1
;
567 oindex
[1] = bMin
? min2
: max2
;
568 write_trx(trxout
, 2, oindex
, atoms
, i
, t
, box
, x0
, nullptr, nullptr);
571 /*dmin should be minimum distance for residue and group*/
572 if (bEachResEachTime
)
574 fprintf(respertime
, "%12e", t
);
575 for (i
= 1; i
< ng
; i
++)
577 for (j
= 0; j
< nres
; j
++)
579 fprintf(respertime
, " %7g", bMin
? mindres
[i
- 1][j
] : maxdres
[i
- 1][j
]);
580 /*reset distances for next time point*/
581 mindres
[i
- 1][j
] = 1e6
;
582 maxdres
[i
- 1][j
] = 0;
585 fprintf(respertime
, "\n");
587 } while (read_next_x(oenv
, status
, &t
, x0
, box
));
605 xvgrclose(respertime
);
608 if (nres
&& !bEachResEachTime
)
612 sprintf(buf
, "%simum Distance", bMin
? "Min" : "Max");
613 res
= xvgropen(rfile
, buf
, "Residue (#)", "Distance (nm)", oenv
);
614 xvgr_legend(res
, ng
- 1, leg
, oenv
);
615 for (j
= 0; j
< nres
; j
++)
617 fprintf(res
, "%4d", j
+ 1);
618 for (i
= 1; i
< ng
; i
++)
620 fprintf(res
, " %7g", bMin
? mindres
[i
- 1][j
] : maxdres
[i
- 1][j
]);
632 int freeLeg
= bMat
? (ng
== 1 ? 1 : (ng
* (ng
- 1)) / 2) : ng
- 1;
633 for (int i
= 0; i
< freeLeg
; i
++)
640 static int find_residues(const t_atoms
* atoms
, int n
, const int index
[], int** resindex
)
643 int nres
= 0, resnr
, presnr
= 0;
644 bool presFound
= false;
647 /* build index of first atom numbers for each residue */
648 snew(residx
, atoms
->nres
+ 1);
649 for (i
= 0; i
< n
; i
++)
651 resnr
= atoms
->atom
[index
[i
]].resind
;
652 if (!presFound
|| resnr
!= presnr
)
662 printf("Found %d residues out of %d (%d/%d atoms)\n", nres
, atoms
->nres
, atoms
->nr
, n
);
664 srenew(residx
, nres
+ 1);
665 /* mark end of last residue */
671 static void dump_res(FILE* out
, int nres
, int* resindex
, int index
[])
675 for (i
= 0; i
< nres
- 1; i
++)
677 fprintf(out
, "Res %d (%d):", i
, resindex
[i
+ 1] - resindex
[i
]);
678 for (j
= resindex
[i
]; j
< resindex
[i
+ 1]; j
++)
680 fprintf(out
, " %d(%d)", j
, index
[j
]);
686 int gmx_mindist(int argc
, char* argv
[])
688 const char* desc
[] = {
689 "[THISMODULE] computes the distance between one group and a number of",
690 "other groups. Both the minimum distance",
691 "(between any pair of atoms from the respective groups)",
692 "and the number of contacts within a given",
693 "distance are written to two separate output files.",
694 "With the [TT]-group[tt] option a contact of an atom in another group",
695 "with multiple atoms in the first group is counted as one contact",
696 "instead of as multiple contacts.",
697 "With [TT]-or[tt], minimum distances to each residue in the first",
698 "group are determined and plotted as a function of residue number.[PAR]",
699 "With option [TT]-pi[tt] the minimum distance of a group to its",
700 "periodic image is plotted. This is useful for checking if a protein",
701 "has seen its periodic image during a simulation. Only one shift in",
702 "each direction is considered, giving a total of 26 shifts. Note",
703 "that periodicity information is required from the file supplied with",
704 "with [TT]-s[tt], either as a .tpr file or a .pdb file with CRYST1 fields.",
705 "It also plots the maximum distance within the group and the lengths",
706 "of the three box vectors.[PAR]",
707 "Also [gmx-distance] and [gmx-pairdist] calculate distances."
710 gmx_bool bMat
= FALSE
, bPI
= FALSE
, bSplit
= FALSE
, bMax
= FALSE
, bPBC
= TRUE
;
711 gmx_bool bGroup
= FALSE
;
714 gmx_bool bEachResEachTime
= FALSE
, bPrintResName
= FALSE
;
716 { "-matrix", FALSE
, etBOOL
, { &bMat
}, "Calculate half a matrix of group-group distances" },
717 { "-max", FALSE
, etBOOL
, { &bMax
}, "Calculate *maximum* distance instead of minimum" },
718 { "-d", FALSE
, etREAL
, { &rcutoff
}, "Distance for contacts" },
723 "Count contacts with multiple atoms in the first group as one" },
724 { "-pi", FALSE
, etBOOL
, { &bPI
}, "Calculate minimum distance with periodic images" },
725 { "-split", FALSE
, etBOOL
, { &bSplit
}, "Split graph where time is zero" },
730 "Number of secondary groups to compute distance to a central group" },
731 { "-pbc", FALSE
, etBOOL
, { &bPBC
}, "Take periodic boundary conditions into account" },
735 { &bEachResEachTime
},
736 "When writing per-residue distances, write distance for each time point" },
737 { "-printresname", FALSE
, etBOOL
, { &bPrintResName
}, "Write residue names" }
739 gmx_output_env_t
* oenv
;
740 t_topology
* top
= nullptr;
744 gmx_bool bTop
= FALSE
;
747 const char *trxfnm
, *tpsfnm
, *ndxfnm
, *distfnm
, *numfnm
, *atmfnm
, *oxfnm
, *resfnm
;
750 int ** index
, *residues
= nullptr;
751 t_filenm fnm
[] = { { efTRX
, "-f", nullptr, ffREAD
}, { efTPS
, nullptr, nullptr, ffOPTRD
},
752 { efNDX
, nullptr, nullptr, ffOPTRD
}, { efXVG
, "-od", "mindist", ffWRITE
},
753 { efXVG
, "-on", "numcont", ffOPTWR
}, { efOUT
, "-o", "atm-pair", ffOPTWR
},
754 { efTRO
, "-ox", "mindist", ffOPTWR
}, { efXVG
, "-or", "mindistres", ffOPTWR
} };
755 #define NFILE asize(fnm)
757 if (!parse_common_args(&argc
, argv
, PCA_CAN_VIEW
| PCA_CAN_TIME
| PCA_TIME_UNIT
, NFILE
, fnm
,
758 asize(pa
), pa
, asize(desc
), desc
, 0, nullptr, &oenv
))
763 trxfnm
= ftp2fn(efTRX
, NFILE
, fnm
);
764 ndxfnm
= ftp2fn_null(efNDX
, NFILE
, fnm
);
765 distfnm
= opt2fn("-od", NFILE
, fnm
);
766 numfnm
= opt2fn_null("-on", NFILE
, fnm
);
767 atmfnm
= ftp2fn_null(efOUT
, NFILE
, fnm
);
768 oxfnm
= opt2fn_null("-ox", NFILE
, fnm
);
769 resfnm
= opt2fn_null("-or", NFILE
, fnm
);
770 if (bPI
|| resfnm
!= nullptr)
772 /* We need a tps file */
773 tpsfnm
= ftp2fn(efTPS
, NFILE
, fnm
);
777 tpsfnm
= ftp2fn_null(efTPS
, NFILE
, fnm
);
780 if (!tpsfnm
&& !ndxfnm
)
782 gmx_fatal(FARGS
, "You have to specify either the index file or a tpr file");
788 fprintf(stderr
, "Choose a group for distance calculation\n");
799 if (tpsfnm
|| resfnm
|| !ndxfnm
)
802 bTop
= read_tps_conf(tpsfnm
, top
, &ePBC
, &x
, nullptr, box
, FALSE
);
805 printf("\nWARNING: Without a run input file a trajectory with broken molecules will "
806 "not give the correct periodic image distance\n\n");
809 get_index(top
? &(top
->atoms
) : nullptr, ndxfnm
, ng
, gnx
, index
, grpname
);
811 if (bMat
&& (ng
== 1))
814 printf("Special case: making distance matrix between all atoms in group %s\n", grpname
[0]);
818 for (i
= 1; (i
< ng
); i
++)
821 grpname
[i
] = grpname
[0];
823 index
[i
][0] = index
[0][i
];
827 GMX_RELEASE_ASSERT(!bMat
|| ng
> 1, "Must have more than one group with bMat");
831 GMX_RELEASE_ASSERT(top
!= nullptr, "top pointer cannot be NULL when finding residues");
832 nres
= find_residues(&(top
->atoms
), gnx
[0], index
[0], &residues
);
836 dump_res(debug
, nres
, residues
, index
[0]);
839 else if (bEachResEachTime
|| bPrintResName
)
841 gmx_fatal(FARGS
, "Option -or needs to be set to print residues");
846 periodic_mindist_plot(trxfnm
, distfnm
, top
, ePBC
, gnx
[0], index
[0], bSplit
, oenv
);
850 dist_plot(trxfnm
, atmfnm
, distfnm
, numfnm
, resfnm
, oxfnm
, rcutoff
, bMat
,
851 top
? &(top
->atoms
) : nullptr, ng
, index
, gnx
, grpname
, bSplit
, !bMax
, nres
,
852 residues
, bPBC
, ePBC
, bGroup
, bEachResEachTime
, bPrintResName
, oenv
);
855 do_view(oenv
, distfnm
, "-nxy");
858 do_view(oenv
, numfnm
, "-nxy");
861 output_env_done(oenv
);
863 for (int i
= 0; i
< ng
; i
++)