[gmx-users] Change in .gro in grompp

Caleb Carlin calebcarlin at gmail.com
Wed Feb 6 02:11:44 CET 2008

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

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

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

Caleb Carlin
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