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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