[gmx-users] zero free energy of ligand in water

Justin Lemkul jalemkul at vt.edu
Sat Mar 12 17:56:21 CET 2016

On 3/12/16 3:43 AM, Sana Saeed wrote:
> hi i have performed simple ligand only simulation (part of protein ligand
> binding free energy calcultaion: alchemical pathway: from complex protein and
> ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result
> i got by using alchemical_analysis.py --> David Mobley's) but the only ligand
> simulation (ligand+water) i am getting zeros for all lambda states. is it
> fine? tahnks in advance

No, that makes no sense.  There should always be some amount of change in the 
free energy during the transformation.



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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