[gmx-users] doubt in minimization part

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 12:34:54 CEST 2012

On 9/28/12 4:25 AM, Shine A wrote:
> Sir,
>     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
> this?

You should have a topology of the system, and .mdp files are provided so you can 
assemble a .tpr file and run minimization.  Individual commands are not provided 
at this point in the tutorial, because (as stated at the beginning of the 
tutorial) it is expected that the user is familiar with a basic Gromacs 
workflow, how to execute grompp and mdrun, etc.

Subsequent minimization steps are performed on system_shrink*.gro files in the 
same manner.


> 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


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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