[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

[Reza Salari]

Hi

I have set up two small systems, one with a single POPC lipid, and another
system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting
charmm ff to gromacs) for my systems. My main question is that for the
single POPC, all the potential energy terms match very well, but for the
membrane system the non-bonding terms differ significantly.

I am providing the full details below and greatly appreciate any hint for
better comparison of the energies.


Thanks,
Reza Salari

Details:

1) Both systems were prepared using VMD "membrane" package:

2)