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

Hicks, Erica erica.hicks at my.und.edu
Fri Jun 8 21:15:11 CEST 2012


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?

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