From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Fri Aug 10 2012 - 12:44:05 CDT
Dear NAMD users,
I have a question regarding how the energies are compared in lammps and namd. I have set the parm (for namd) compatible with my lammps data file but I get different energies (even for bond and angle the energy that I get in namd is much lower than lammps). The structures are exactly the same and I want to make sure I get the same initial energies (at least close) in the two packages (I tried this with a simpler system containing only one molecule but namd gives an error of " Periodic cell has become too small for original patch grid" which I couldn't solve by increasing the margin or use "useFlexibleCell no" command). Can anyone make a comment please?
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