[gmx-users] Problem in Free Energy Calculations

Justin Lemkul jalemkul at vt.edu
Thu Dec 31 17:25:58 CET 2015

On 12/31/15 11:19 AM, shagun krishna wrote:
> Hii Justin,
> I am using the old version of gromacs i.e 4.6.5 and the tutorial that I am
> following is also compatible with the same version. Then too I am getting
> the problem.

If you upgrade to the current version, your life will be a lot easier.  The 
4.6.5 version of the tutorial used some crude scripting to make things work; it 
could be more elegant but I'm afraid I do not have time to troubleshoot outdated 
information.  I intend on taking the old versions of the tutorials offline, anyway.

> One more thing if I got the energy for the ligand and the protein how would
> I combine them to single .edr file since gmx lie program uses a single file
> such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr
> <http://manual.gromacs.org/online/edr.html> file. and How I will get the
> values of  Elj, Eqq, Clj, Cqq.

If you're doing a real free energy calculation, I don't see why you would want 
to do this.  There's plenty of literature out the LIE method, though.  But it 
requires two simulations (not using the free energy code): protein-ligand and 
ligand in water.  The interaction energies come from energygrps in the .mdp 
file, so you have everything you need in one .edr file; you do not need the 
energy of the protein and energy of the ligand separately.  You need the 
nonbonded interaction energy between them (as well as the ligand-water 
interaction energy from the second simulation).



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


More information about the gromacs.org_gmx-users mailing list