On 8/23/13 9:21 AM, Rama wrote:
Hi Justin,
Thanks for Kalp15-DPPC Bilayer tutorial.
I'm doing MD simulations for MMP protein-DMPC bilayer (128 lipids) complex
by following your protocol. I'm not familiar with MD simulation parameters.
Should I need to change any parameters in npt.mdp , nvt.mdp and md.mdp files
or somewhere else.
Lipids can be exceptionally tricky to get right. If you're not familiar with
what the settings are and what they do, please invest some time in reading about
advances in methods and force fields. My tutorial is just one example of how
things can be done, but the force fields used are fairly old and better ones,
requiring entirely different settings, exist.
At minimum, clearly one would need to change DPPC in tc-grps to DMPC, and since
the phase transition temperature of DMPC is lower than DPPC, there is no need to
run the simulation at 323 K.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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