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

Qiong Zhang qiongzhang928 at yahoo.com
Tue Mar 9 09:27:11 CET 2010

Hi dear Mark,

Thanks very much for your reply.

Yes, you are right that I am using PME. 

The molecules I am simulating are carbohydrates. And I am using Glycam06 Force Field. 

The interaction energy I got previously is analyzed by directly using g_energy, summing up Coul_SR and LJ_SR of two groups. 

In order to include the long range interaction, I've also tried "mdrun -rerun" option.  So three "reruns" were carried out for molecule 1(1st), molecules 2 (2nd) and molecule 1 and 2 (3rd). This time, I found the long range Coul_recip between molecule 1 and 2 is a quite positive value. So when only Coul_SR is included, the electrostatic interaction between molecule 1 and molecules 2 is much more negative (> 100 kj/mol) than that when both Coul_SR and Coul_recip are included. I guess, for such carbohydrate molecules, long range Coul_recip can not be excluded. 
Am I right here? 

For the second summing up problem, I am still checking all the input file, especially the index file. 

Thank you very much!


----- 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
> 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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