[gmx-users] free energy problem

[Justin Lemkul]

On 10/19/14 5:14 AM, elham tazikeh wrote:
> Dear Justin
> thanks for your replys and your patient
>
> i think my main  problem is the way of using of perl/shell scripts in your
> tutorial (Free energy for methane)
>
> my question is: for script using, i must be execute them by *(chmod +x
> ...) * and then use of this command (*perl write_mdp.pl
> <http://write_mdp.pl> em_steep.mdp * or
> *sh write_sh.pl <http://write_sh.pl> em_steep.sh*) ? are they correct?
>
> in this tutorial, its up to us that choose of *perl scripts *or *shell
> scripts* without any difference?right??
>

No.  It's a Perl script, executed with the Perl interpreter, and you're also 
mixing and matching file names incoherently.  The "write_mdp.pl" script modifies 
.mdp files to give you a series of inputs.  The "write_sh.pl" script writes a 
series of job files that execute the runs.

perl write_mdp.pl em_steep.mdp

No invoking chmod, no executing via sh, and no use of anything called 
"em_steep.sh," which doesn't even exist in my tutorial.

> at the end, script files read from mdp files without any changes or
> rep0lacing by values by us...is it correct?
>

The script does all the work for you.  All it does is replace the integer values 
of init_lambda_state to save you some time.  It's very tedious (though trivially 
simple) to copy the input files to new names and specify the correct array 
index, so the script saves you some time.

-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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