[gmx-users] Change in .gro in grompp

[Mark Abraham]

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