[gmx-users] Vizualization of lipid protein system

[Justin Lemkul]

On 3/14/16 7:48 AM, James Starlight wrote:
> Dear all!
>
> I am looking for the possibility to vizualize my long md trajectory
> for the receptor embedded in the membrane
>
> If I just load the trajectory to vmd there is no problem with the
> exeption that receptor moves laterally along the membrane resulting at
> the end in PBC artifacts
>
> If It try to post-process the trajectory by the following method
>
> g_trjconv -s minimization.gro -f production_run_gpcr_CG -dt 10 -b 100
> -o traj.dcd  -pbc nojump
>
> the system now becomes centred on the receptor but all lipids now are
> fly away from the receptor which looks not very good for me =)
>
>
> how I could prevent those artifacts making vizualisation properly7
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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