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

Justin Lemkul jalemkul at vt.edu
Wed May 1 02:33:27 CEST 2013

On 4/30/13 4:19 PM, Reza Salari wrote:
> 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)

It appears you hit "send" too early.  Please provide the entirety of the details 
you intended.  Complete .mdp files and actual quantification of the differences 
you are observing are also very important.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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