[gmx-users] LIE calculations

sai nitin sainitin7 at gmail.com
Mon Aug 20 19:46:53 CEST 2012

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 ??

Can anybody please help



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