[gmx-users] Analyzing Desmond trajectories using GROMACS tools

[Justin Lemkul]

On 3/3/17 11:28 AM, zeineb SI CHAIB wrote:
> Dear gmx users,
>
> I'm running simulations on membrane proteins (POPC) using Desmond software and I would like to use GROMACS tools to analyze certain parameters related to the membrane. Exemple:
> - Deuterium order parameters of the acyl chains
> - Density of the membrane environment
> - Area per lipid headgroup
> - Bilayer thickness
> - Lateral diffusion of the lipids
>
> Some files are easy to generate using VMD (.trr, .gro files) but I'm having difficulties to generate a tpr file.
>
> Could you help me with any available tools please.
>

You need to generate a topology for the system and then run the system through 
grompp with any .mdp file (the contents are irrelevant if you're only using it 
for analysis, it just has to be syntactically correct).  Consult any basic tutorial.

-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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