[gmx-users] MD for extracellular and transmembrane system

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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