[gmx-users] Change in .gro in grompp

[Justin A. Lemkul]

Quoting Caleb Carlin <calebcarlin at gmail.com>:

> 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.  The processed topology is correct,
> but the output configuration isn't accessible and mdrun doesn't produce a
> trajectory file for a canceled run.

Try setting nstxout = 1.

> 1. Is there a way to check the configuration of a system after running
> grompp?

Try ngmx, using your input .gro and .tpr files.

>
> 2. Is there a reason grompp would drastically change the configuration of a
> system?

It wouldn't; I suspect an incorrect topology or perhaps poor minimization, but
it is difficult to say.  Perhaps the slabs being "pushed together" is an
artifact of periodic boundary conditions, and is unrelated to your crash.  See
here:

http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

-Justin

>
> I am using Gromacs 3.3.1 and can supply any or all of the input files upon
> request.
> Thank you for any assistance
>
> Caleb Carlin
>



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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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