[gmx-users] gromacs.org_gmx-users Digest, Vol 123, Issue 124: reply to message 1
Guilherme Duarte Ramos Matos
gduarter at uci.edu
Thu Jul 24 22:09:24 CEST 2014
Thanks for the reply!
I actually managed to solve this issue. I was building the super cell
with Mercury, the Cambridge Crystallographic Database software, but I
was not aware of connectivity issues that appeared when I built the
crystal with fragments of molecules. It was solved easily with a
different option in the packing/ slicing utility.
Thanks!
~ Guilherme
*****************************************************
Guilherme D. R. Matos
Graduate Student at UC Irvine
Mobley Group
*****************************************************
On Wed, Jul 23, 2014 at 2:48 AM,
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
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> 1. Re: Molecular Solid PBC problem (Justin Lemkul)
> 2. about cos-accelation (Hyunjin Kim)
> 3. g_energy questions (Andy Chao)
> 4. Re: Error in system_inflate.gro coordinates does not match
> (RINU KHATTRI)
> 5. Angle group (Cyrus Djahedi)
> 6. Re: about cos-accelation (Dr. Vitaly Chaban)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 22 Jul 2014 20:15:23 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Molecular Solid PBC problem
> Message-ID: <53CEFE9B.4010801 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 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
>
> ==================================================
>
>
>
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