On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote:
Thank Justin ! That is APL. How about bilayer thickness ? I made
density.xvg file of headgroup from using g_density.
g_dist with index groups specifying however you want to define the boundaries
for the membrane, or (shameless plug) a lateral projection of thickness (from
which an average can easily be derived: http://bevanlab.biochem.vt.edu/GridMAT-MD/.
-Justin
On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul <[email protected]> wrote:
On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:
Dear All,
I want to know that my lipid bilayer is equilibrated or not yet. So i want
to calculate the change of area per lipid and the bilayer thickness versus
time.
Which tool or method should i use ?
Extract box vectors over time from the .edr file, then use a script of
your own creation to multiply them and divide by the number of lipids per
leaflet. Of course, that goes out the window if there is a protein present.
-Justin
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