[gmx-users] problem with interaction energy calculated by g_energy

Qiong Zhang qiongzhang928 at yahoo.com
Mon Mar 8 10:34:07 CET 2010

Dear gmx users,

I am studying the adsorption behavior of a molecule ( molecule 1) on a surface (molecules 2). Based on the production run, I calculated the interaction energy between molecule 1 and molecules 2 by g_energy. 
Here comes the first question: Why only short range interactions between 1 and 2 are displayed, namely, Coul_SR and LJ_SR? So the interaction energy E 1_2 I calculated is just the sum of Coul_SR+LJ_SR. Will this bring about huge errors?

After this, I'd like to know the individual contributions of the components of molecule 1  to the interaction energy between 1 and 2. For example, molecule 1 is composed of A, B, C and D resdues. So again, by g_energy, I got interaction energy between A, B, C and D with 2, respectively, denoted by E A_2, E B_2, E c_2 and E D_2. Still, these interaction energies are the sum of  Coul_SR+LJ_SR.
Then comes the second question: Why the sum of E A_2, E B_2, E c_2 and E D_2 does not equal to E 1_2? I found there was big difference between them, sometimes as large as 50 kJ/mol. 

Could anybody give me some hints or suggestions please?

Thank you very much in advance!

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