[gmx-users] confout.gro

[Justin Lemkul]

On 7/5/14, 12:51 AM, RINU KHATTRI wrote:
> hello gromacs users
> but i am confussed if confout.gro is input, in which step it is formed
> according to tutorial before this step the step is
> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
> is system_inflated.gro is confout.gro or which gro file i must be used
> as confout.gro
>
> perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5
> area_shrink1.dat

The file "confout.gro" is the default name of the final output coordinates of an 
mdrun process, unless you provide a different file name to mdrun -c.  In this 
case, the protocol is:

1. Inflate the system (produce system_inflated.gro)
2. Minimize the inflated system (produce confout.gro, unless otherwise named)
3. Begin shrinking the system, starting with the output of step 2.

So "confout.gro" is the _output_ of step 2 and the _input_ of step 3.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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