[gmx-users] LIE calculations

[Justin Lemkul]

On 8/20/12 1:46 PM, sai nitin wrote:
> Dear all,
>
> Recently i performed 10ns protein ligand simulation and also ran 10ns
> simulation only for ligand in solvent obtain parameters for g_lie to
> determine DGBind values.
>
> I calculated  -Elj -Eqq values from ligand only simulation energy
> file... this is where im stuck :(
>
> -Elj =   Lennard-Jones interaction between ligand and solvent
> -Eqq = Coulomb interaction between ligand and solvent
>
> Im not clear which energy terms should be taken for g_lie caluclation
>
> LJ-SR: LIG-rest or LJ-LR: LIG-rest or LJ-l4:LIG-rest  for -Elj ??
>
> Coul-SR:LIG-rest or Coul-l4 : LIG-rest for -Eqq ??
>

1-4 interactions are intramolecular.  These terms should be equal to zero.

Note that if you used PME for any of these calculations, you will have to use 
the mdrun -rerun feature with a modified .mdp file.  This topic has been 
discussed within the last few days on this list.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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