----- Original Message -----
From: Moeed <[email protected]>
Date: Wednesday, June 16, 2010 8:29
Subject: [gmx-users] nonbonded energy contributions
To: [email protected]
> 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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