[gmx-users] doubt in minimization part

Shine A shine.a at iisertvm.ac.in
Fri Sep 28 10:25:27 CEST 2012


   I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
Now I am confusing with the following ( shown at botom) part of the
tutorial.Here minimization means to minimize system_inflated.gro, is it
right? Then without .epr and .top files of system_inflated.gro how can I do

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

Note how many lipids were deleted and update the [ molecules ] directive of
your topology accordingly. Run energy minimization. Then, scale down the
lipids by a factor of 0.95 (assuming you have used default names, the
result of the minimization is called "confout.gro"):

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat

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