[gmx-users] Energy Minimization - not getting correct lipid area

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 8 21:20:36 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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