[gmx-users] error about g_bar

Justin Lemkul jalemkul at vt.edu
Tue Aug 19 13:57:27 CEST 2014

Please keep the discussion on the mailing list.

On 8/19/14, 6:01 AM, Swapnil Kate wrote:
> hello Justin,
> Now I have 5 compound system in which one is solvent (n decane) (non
> disappearing). I want to calculate free energy of the other compounds. In which
> I want to show two molecules are disappearing and along the way two new
> molecules are forming, so can we do this type of work on GROMACS?

Not sure, but my guess is no, not simultaneously.  You can, of course, transform 
each of the molecules individually or do the disappearing molecules in one 
procedure (with a custom [moleculetype] containing both molecules) and the 
appearing molecules in another (same approach) and sum the free energy change. 
I don't know if that will be equivalent to what you're needing to do, though.



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


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