[gmx-users] converting Desmond trajectories to Gromacs

[Justin Lemkul]

On 7/24/12 6:13 AM, Nidhi Jatana wrote:
> Dear Sir/Madam
> I am running simulations on a membrane protein using Desmond and I
> want to calculate area per lipid for the entire trajectory. I can
> convert the trajectories to those of Gromacs using VMD. What else do I
> need in order to calculate area per lipid using Gromacs?
>

The area per lipid is not a trivial quantity to calculate when there's a protein 
involved, and there is no Gromacs tool that will do it.

We created a program a few years ago that does, but note that you cannot analyze 
a trajectory, only a single coordinate file (.gro or .pdb).  The current 
workaround is to dump out a series of coordinate files and loop over all of them 
in a shell script.  Note that, depending on how many frames you have in your 
trajectory, this may take quite a while - APL calculations typically take on the 
order of 2-5 minutes (per frame), depending on how large the system is.

http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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