[gmx-users] free energy question

[Justin Lemkul]

On 10/19/14 11:31 PM, elham tazikeh wrote:
> Dear Justin
> Your mean is, i should use:
> perl write_mdp.pl em_steep.mdp
> For creating *.mdp files for EM process per lambdas
>
> And for producing for example nvt.mdp,i must write:
> perl write_mdp.pl  nvt.mdp ?
>

Yes, which is exactly what is stated on 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html

> Also for acheiving neccesary files for run process we need to shell files
> ...but i dont know about writing and accessing to job_*.sh?
>

The process is identical, just with different file names:

perl write_sh.pl job.sh

-Justin

-- 
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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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