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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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