On 6/8/12 3:15 PM, Hicks, Erica wrote:
Hi,
I am working through the KALP-15 tutorial and having difficulties getting the
correct area per lipid (~71 A^2). I first scaled the lipid by a factor of 4
(perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) then
did energy minimization (mdrun -v -deffnm em) and then scaled down by 0.95 (perl
inflategro.pl em.gro 0.95 DPPC 0 system_shrink.gro 5 area_shrink1.dat). The
tutorial then said to do energy minimizations and scale by 0.95 until the
correct area per lipid is reached. When I do, my numbers stay the same, i.e. all
three are 0.583197761890625 nm^2. Any suggestions?
After how many iterations? If you've hit 0.58 nm^2, you've gone too far.
You'll likely hit a point where you can't squeeze the lipids any more, but 25-26
iterations consistently gives the value stated in the tutorial.
-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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