[gmx-users] Change in .gro in grompp
Mark.Abraham at anu.edu.au
Wed Feb 6 02:32:14 CET 2008
Caleb Carlin wrote:
> 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 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?
> I am using Gromacs 3.3.1 and can supply any or all of the input files
> upon request.
> Thank you for any assistance
More information about the gromacs.org_gmx-users