[gmx-users] Molecular Solid PBC problem

[Guilherme Duarte Ramos Matos]

Dear GROMACS user community,

I'm working with molecular dynamics of molecular solids and I am having
trouble to set up the calculations.

I got the crystal structure's pdb file from the Cambridge Database and used
editconf to generate the coordinate file. The topology file is really
simple: it just carries the hamiltonian of an Einstein crystal, that is,
harmonic potentials binding each atom of the molecule to its lattice
position. The relevant part of the mdp file is:

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 1
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = xyz
; nblist cut-off
rlist                    = 1.0

Unfortunately, after running grompp, I get the following warning:

 WARNING 1 [file molecule_ideal.top, line 351]:
  10116 non-matching atom names
  atom names from molecule_ideal.top will be used
  atom names from input.gro will be ignored

The funny and worrying part of this problem is that all the atom types were
changed in the output of mdrun. The simulation just didn't crash because of
the hamiltonian used. I investigated a little bit and it seemed that
GROMACS was not able to connect the fragments in the wall to their
neighboring periodic copies. That happened because fragments were numbered
as distinct molecules. Check this small portion of the coordinate file:

   35RES     C1  211   0.017   5.561   4.241
   35RES     N1  212   0.033   5.362   4.363
   35RES     O1  213   0.145   5.367   4.163
   35RES     C2  214   0.074   5.421   4.245
   35RES     H1  215   0.057   5.283   4.386
   35RES     H3  216   0.087   5.628   4.238
   36RES     C1  217   0.017   5.561   5.526
   36RES     N1  218   0.033   5.362   5.648
   36RES     O1  219   0.145   5.367   5.448
   36RES     C2  220   0.074   5.421   5.530
   36RES     H1  221   0.057   5.283   5.671
   36RES     H3  222   0.087   5.628   5.523
   37RES     C1  223   0.017   5.561   6.811
   37RES     N1  224   0.033   5.362   6.933
   37RES     O1  225   0.145   5.367   6.733
   37RES     C2  226   0.074   5.421   6.815
   37RES     H1  227   0.057   5.283   6.956
   37RES     H3  228   0.087   5.628   6.808
   38RES     C1  229   0.753   0.786   1.671
   38RES     N1  230   0.770   0.587   1.793
   38RES     O1  231   0.882   0.592   1.593
   38RES     C2  232   0.811   0.646   1.675
   38RES     O2  233   0.636   0.631   1.973
   38RES     C3  234   0.687   0.665   1.868
   38RES     C4  235   0.672   0.798   1.799
   38RES     H1  236   0.794   0.508   1.816
   38RES     H2  237   0.696   0.797   1.593
   38RES     H3  238   0.824   0.852   1.668
   38RES     H4  239   0.707   0.870   1.855
   38RES     H5  240   0.579   0.817   1.779

The molecule number 38 has 12 atoms and is inside the walls while 35, 36
and 37 have 6 atoms each, represent similar fragments, along the wall but
are accounted as isolated molecules.

Does anyone have a suggestion to help me with this problem?
Thank you in advance.

~ Guilherme

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Guilherme D. R. Matos
Graduate Student at UC Irvine
Mobley Group

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