[gmx-users] (no subject)

[Justin Lemkul]

On 11/9/14 2:20 PM, Thomas Lipscomb wrote:
> Ok I figured out half of it:
>
> perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat
> perl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat
> etc
>
> But if I have to minimize inbetween those steps I am not clear how to connect mdrun minimization with inflategrow:
>
> perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat
> mdrun -s topol.tpr -v
>
> perl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat
> mdrun -s topol.tpr -v
>

Well, you have to run grompp in between to generate a .tpr with the new 
coordinates.  Your topology is always the same, the .mdp file is always the 
same, the only thing you're changing are the coordinates, which need to be 
minimized at each step.

If these concepts aren't clear, back up and do some more basic tutorial(s) 
before doing something complex.  Learn to walk before you try to run.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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