[gmx-users] nonbonded energy contributions

[Moeed]

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).

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.

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?

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
=...

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...!

Thank you for your time :)
MOeed
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