[gmx-users] Plotting area per lipid along time
jalemkul at vt.edu
Sun Oct 21 16:26:06 CEST 2012
On 10/21/12 8:47 AM, Shima Arasteh wrote:
> Would you please give me an advice to get area per lipid plot as a function of time?
> I'm only able to get area per lipid from the .gro file of mdrun, but I don't know if it is possible to see the all area per lipids along the time?
If you have a pure lipid system, then APL is calculated as the product of the
x-y box vectors (assuming that the membrane is in the x-y plane) divided by the
number of lipids per leaflet. This method does not allow you to obtain the
areas contributed by each individual lipid. If you have a protein present,
there is no Gromacs tool that will allow you to do this calculation at all
because you need the area of the protein.
If you are using our GridMAT-MD program, you can loop the script over individual
snapshots using simple shell scripting. We intend to include trajectory support
at some point in the future, but none of the current developers have much time
to work with it right now.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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