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 Thanks, Nitin -- -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
