Re: I have a question about pair interaction energy calculations.

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Oct 31 2013 - 13:21:31 CDT

That's hard to answer. Possible explanations include:
- using a methodology for calculation the interaction energy that flips
the sign
- having a mistake in the atom selection

It should also be noted that dividing the interaction energy like this is
not very meaningful because of the way charges in the force field are
optimized; they reproduce the electrostatic potential around the entire
group relatively well, but the point charge of each individual atom is not
necessarily physically meaningful. In this sense, it would be better to
calculate the interaction with the entire -CH2-N(CH3)3 group (yes, do
include the CH2) at once.

And even then, you'll have a quantity that can be correlated to few
real-life observables; for more info on this, search this list's archive
for a discussion with subject "NAMD electrostatic interaction Failure"
that took place near the end of last month.

On 10/30/2013 03:14 AM, 송 연호 wrote:
> Dear all
>
> Hello.
>
> I have a question about pair interaction energy calculations for my system
> that is composed of one K+, 80 DMPC lipids and several thousand water
> molecules.
>
> I have calculated the pair interaction energy between +1 charged atom (K+
> ion) and -0.6 charged atoms (N atoms at head group of 80 DMPC lipids),
> Distance between two molecules is approximately 25 Å. The calculation
> shows that electrostatic energy**is nearly +128 kcal/mol/Å.
>
> I have also calculated the pair interaction energy between +1 charged atom
> (K+ ion) and total +0.4 charged groups ((CH3)3 groups at head group of 80
> lipids), Distance between two molecules are nearly 25 Å. The resulting
> electrostatic energy is around -256 kcal/mol/Å.
>
>
> I don’t understand these two results. I'm wondering why the electrostatic
> interaction energy between + and - charged atoms has a positive value and
> the one between + and + charged groups has a negative value
>
> The net-charge of my system is +1 (because of a k+ ion) and I use PME
> parameters. The force field that I used is CHARMM27 for all the atoms.
>
> Thanks in advance
>
> Yeonho Song.
>
>
>

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:55 CST