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
--
========================================
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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