On 6/1/14, 3:51 AM, rahul dhakne wrote:
Dear all Gromacs user,
I am knew to Gromacs for molecular dynamics. One off the hurdle I
encountered is that can I use GROMACS for modelling protein with
extracellular and transmembrane domain i.e., maintain water/lipid system in
molecular dynamics simulation. Can I add the water system for extracellular
domain and lipid system for transmembrane domain in GROMACS? if yes please
provide necessary information.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
Choose a force field carefully. There are many options. The tutorial
illustrates on simple approach, but there are other parameter sets that may be
more suitable, depending on your system.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul
==================================================
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