From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 10 2012 - 15:56:18 CDT
On Fri, Aug 10, 2012 at 7:44 PM, Jacqueline Schmidt
> 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
please note that CHARMM and LAMMPS have different conventions
as to how several parameters have to be specified. i've made tests in
the past and bonds and angles as well as non-bonded can be made
to be a perfect match. the only issues are with dihedrals. LAMMPS
doesn't have CMAP and has a strange way to handle 1-4 exclusions
and dihedrals that are specified multiple times.
> 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?
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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