[gmx-users] LIE method

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Sun Jan 12 06:17:04 CET 2014

dear Justin thanks for your reply
is the rerun energies needed only for protein ligand complex? do the ligand in water simulation need the rerun energies?
thanks a lot

On Sunday, January 12, 2014 1:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote:
> hi dear GMX users
> I simulated protein-ligand complex for 20 nanoseconds. I want to calculate free energy by LIE method so I simulated ligand in water in the same conditions. I used PME and full periodic boundary conditions in my simulations so I wrote a new .mdp file that didn't use PME (I used cut off) and used following command for protein-ligand complex simulation:
> mdrun -s newtpr.tpr -rerun full20ns.xtc
> then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command.
> are these steps sufficient. is the stage or another commandnecessary?

If the protein-ligand simulation was done with PME as well, then you need to get 
the rerun energies, as well.



Justin A. Lemkul, Ph.D.
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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