[gmx-users] LIE calculations
sainitin7 at gmail.com
Mon Aug 20 19:46:53 CEST 2012
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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