[gmx-users] Electrostatic interaction energy

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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