[gmx-users] Electrostatic interaction energy

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 8 17:09:25 CEST 2012

On 6/8/12 11:04 AM, Turgay Cakmak wrote:
> Hi all,
> I have 2 questions related to the electrostatic energy of the system..
> 1) Is *total electrostatic energy* equal to *Coulomb-(SR)* + *Coul.-recip*. OR
> *Coulomb-14* + *Coulomb-(SR)* + *Coul.-recip*. I am so confused.

The total electrostatic energy is the sum of all Coulombic components.  Whether 
that is relevant is up to you.

> I specified in my .mdp file;
> coulombtype = PME
> rvdw = 1.0
> rlist = 1.0
> rcoulomb = 1.0
> fourierspacing = 0.16
> pme_order = 4
> ewald_rtol = 1e-5
> 2) I want to calculate electrostatic interaction energy between 2 residues in my
> system which has 10 peptides in total. But I think, I should have specified the
> energy groups composed of that 2  residues in my mdp file before starting the
> simulation. So in this case, is there any way to get this interaction energy OR
> can I just calculate the electrostatic energy of the whole system?

Yes, to get an energy decomposition between two residues you need to specify 
appropriate energygrps.  You can create a new .tpr file and back-calculate these 
quantities using the mdrun -rerun feature.  Be aware though, that the PME 
reciprocal term cannot be (easily) decomposed and the best you can do is 
calculate short-range nonbonded energies between your chosen groups.  Whether or 
not that is useful is something you must demonstrate.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list