[gmx-users] LIE method

[Mahboobeh Eslami]

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

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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