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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