[gmx-users] Molecular Solid PBC problem

[Justin Lemkul]

On 7/22/14, 7:53 PM, Guilherme Duarte Ramos Matos wrote:
> 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

As it should; gromp warned you that a huge number of atoms were out of order 
with respect to the topology, so the topology is used, and the identity and/or 
types of the atoms are changed accordingly.

> 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:
>

How did you generate the original topology?  The mismatch between coordinates 
and topology could also be causing issues with bonded geometry, because 
everything is likely to get scrambled.

>     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?

If you can provide the exact details of what these molecules are and how you 
generated the topology, probably, but without that information it's a bit hard 
to suggest anything.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================