[gmx-users] free energy for ethanol

Justin Lemkul jalemkul at vt.edu
Sat Oct 18 12:14:53 CEST 2014

On 10/18/14 1:38 AM, elham tazikeh wrote:
> Dear Justin
> i really appriciate for your reply
> i trying to follow this tuturial about free energy of ethanol:
> *http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf
> <http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf>*
> there was* mklambda.sh* in that tutorial
> when i used above command for creating different lambdas:
> *sh mklambdas.sh run.mdp topol.top equil.gro*
> i  will receive this error:
> *mklambdas.sh: 12: Syntax error: "(" unexpected*
> how can i fix it?

No idea.  It works for me.  Perhaps you're running some ancient version of your 
shell that requires different syntax.

> about your tutorial (methane), you said , you must change some sections
> i follow your tutorial but received empty files for every lambdas...
> could you please send me some tutorials for practicing this issue (Free
> Energy Calculation)?

The only tutorial I have is the one that's online.  It seems your problem is in 
getting simple shell and Perl scripts to work, which is an issue regarding your 
workstation and is external to either tutorial.



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


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