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