[gmx-users] Molecular Solid PBC problem
Dr. Vitaly Chaban
vvchaban at gmail.com
Wed Jul 23 11:54:06 CEST 2014
You can see in the topology file whether gromacs wrote down bonds
responsible for periodicity.
Coordinate file says nothing in this regard.
Good luck.
Dr. Vitaly V. Chaban
On Wed, Jul 23, 2014 at 1:53 AM, Guilherme Duarte Ramos Matos
<gduarter at uci.edu> 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
> 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
>
> *****************************************************
> Guilherme D. R. Matos
> Graduate Student at UC Irvine
> Mobley Group
>
> *****************************************************
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