01 January 1970 1 10K Report

I have a modeled protein 3D structure with tow cofactors.When i do molecular dynamics simulation  whit gromacs, distances between them increase up to 9 A .while their distances after homology modeling was 3A. i freezed 2 cofactors and 1 aminoacid  white freezegrps in .mdp file.Now their distances are normal and ok, but now potential energy of molecule is a positive number instead of being a minus one. any suggestion? it is a terrible problem. pleas help me.

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