[gmx-users] nonbonded energy contributions

Mark Abraham mark.abraham at anu.edu.au
Wed Jun 16 01:01:38 CEST 2010

----- Original Message -----
From: Moeed <lecielll at googlemail.com>
Date: Wednesday, June 16, 2010 8:29
Subject: [gmx-users] nonbonded energy contributions
To: gmx-users at gromacs.org

> Hello Dear users,
> I appreciate your help with the following issues.
>  I am trying to extract interaction energies (non bonded) between hexane
>  molecules (vdw and electrostatics). I have used rerun program to exclude
>  intramolecular non bonded terms. In litrature people calculate these energies from vdw and electrostatics but 
> still I do not have a clear image on details of energy contributions. In GROMACS thre are good many options like SR, LR (PME/ dis correction).

Well that's your job to do some background reading. The GROMACS manual is a wonderful place to start. You will notice immediately that people in the literature were not using PME. There's an excellent reason for that, which follows immediately from how PME works.
> 1-Can you please guide me for my hydrocarbon system what would be the best approach to get interaction energies? below are the enrgy terms I have at the moment. Do I need to include disp. corrections as well?
> Please help me with excluding or includeing PME and disp.corr contributions.

You should read what these are about and make your own decision. You won't learn any other way :-)

>     	 	 	 	 	<!-- 		@page { margin: 2cm } 		P { margin-bottom: 0.21cm } 	--> 	  > Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
 > ------------------------------------------------------------------------------
 > Angle                       4400.09 

 > Ryckaert-Bell.              1009.62 

 > LJ-14                       648.411 

 > Coulomb-14                 -278.654 

 > LJ (SR)                    -3010.16 

 > Coulomb (SR)                74.7846 

 > Coul. recip.               -78.0436 

 > Potential                   2766.05 

>  2- I have use nrexcl 7 in top file but I am still getting 1-4 interactions in breakdown! why is this heppening?

1-4 interactions are considered bonded, so nrexcl has no effect. You need to use gen-pairs = no, or zero out the fudgeLJ/QQ terms, or not use [pairs]

> 3- To calculate interaction energies can I sum up the energy contributions ? for example 
 > LJ-14                       648.411 + Coulomb-14                 -278.654 +LJ (SR)                    -3010.16 +Coulomb (SR)                74.7846 =...
Yes. Whether this means anything is up to you :-)

> 4- About viewing the results: How can I plot the energy or force... vs. time ( graph)? I have found the program g_traj but it just lists the values ..no graph...!

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