[gmx-users] Change in .gro in grompp

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Feb 6 09:14:38 CET 2008

Hi Caleb,

You can use editconf to extract the coordinates from your .tpr file
(but these will be the same as those in the input file used).
My guess (and Mark's) is that you placed a slab on either extreme of
your unitcell, which makes them occupy the same space in the infinite
simulation system. If you have these slabs parallel to the xz plane
and have an x-vector of length 10, you should make sure to have the
first slab at say x=0.0 and the second at x=10.0-d, where d would be
the distance you want to have them at.
On the other hand, you could think "why bother?". Your slab will
probably have two equivalent sides, so it should be much the same
thing if a molecule would bind on one side or the other.



On Feb 6, 2008 2:32 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Caleb Carlin wrote:
> > Greetings,
> > I am simulating tip4p-ICE between two slabs of silicon.  Prior to using
> > grompp, the configuration renders correctly in VMD and appears as intended.
> > After using grompp and mdrun, the system errors out with LINCS errors.
> > The recorded configuration steps show the silicon slabs pushed together
> > in the middle with the water on either side.
> If you're using a periodic system, then this could be equivalent to what
> you had all along. Two discontiguous slabs of silicon at a periodic
> boundary are one slab of silicon...
> > The processed topology is
> > correct, but the output configuration isn't accessible
> What does this mean?
> > and mdrun doesn't
> > produce a trajectory file for a canceled run.
> > 1. Is there a way to check the configuration of a system after running
> > grompp?
> grompp doesn't change anything. It synthesizes your input .mdp,
> configuration file, and such.
> > 2. Is there a reason grompp would drastically change the configuration
> > of a system?
> No.
> > I am using Gromacs 3.3.1 and can supply any or all of the input files
> > upon request.
> > Thank you for any assistance
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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