I am trying to simulate biomolecule in Guanidinium chloride in
AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking
the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in
energy minimization step but in NVT step files are generated and shows
segmentation fault(core dumped). How to solve this problem?
I have verified the topology of GdmCl by matching the density with the
experimental density. My another question is that should I proceed with the
topology by matching density only? Looking for some suggestions.
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