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

Mark Abraham mark.abraham at anu.edu.au
Mon Mar 8 23:57:21 CET 2010

----- Original Message -----
From: Qiong Zhang <qiongzhang928 at yahoo.com>
Date: Monday, March 8, 2010 20:35
Subject: [gmx-users] problem with interaction energy calculated by g_energy
To: gmx-users at gromacs.org

| > 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?

Guessing wildly (since you've not told us the nature of your simulation protocol) you're using PME, and so the long-range contributions cannot be decomposed group-wise. This is probably a good thing - I'm not aware of any force field that has been parameterized so that small chunks of atoms interaction energies correlate to anything useful.

> 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 
> 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?

They should add up. Check your index group definitions and use in the .mdp file.


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