[gmx-users] doubt in minimization part
jalemkul at vt.edu
Fri Sep 28 12:34:54 CEST 2012
On 9/28/12 4:25 AM, Shine A wrote:
> 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
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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users