[gmx-users] nonbonded energy contributions

[Mark Abraham]

----- 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...!
http://www.gromacs.org/Documentation/How-tos/Graphing_Data
Mark
 

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