[gmx-users] query for binding energy

devawati dutta devawatidutta at gmail.com
Wed Jan 12 13:21:28 CET 2011

Dear Sir,
               I have simulated my protein ligand complex without using PME
but with cut-off as  coulombtype parameter. With g_energy command I am
getting the value of non-bonded interactions as follows:
   Interaction LJ-SR      LJ-LR    Coul-SR     Coul-LR P+L(bound) -113.2000
-8.1800 -15.0650 6.7500 L+S(bound) -93.4900 -10.2900 -18.5400 -2.2700





And I calculated the binding energy through LIE and I got binding energy=
-5.17 Kj/mol. I need the value in Kcal/mol. And after converting the valu in
Kcal/mol, its a very small value of -1.23 Kcal/mol.I think its not a correct
value. Am I getting the right values for the non-bonded Intearctions? Or I
should get higher values (for LJ and Coul). I am unable to understand what
fault I am doing? Please help me out.

Your's sincerely
Devawati Dutta
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