[gmx-users] Coul-SR: positive value for interating group
mark.j.abraham at gmail.com
Wed May 27 15:11:11 CEST 2015
Indeed. Many force fields in common use are additive, but this is not the
same as decomposable!
On Wed, May 27, 2015 at 2:52 PM André Farias de Moura <moura at ufscar.br>
> just guessing, based on the few informations you posted: if the local
> dipole moments of these groups are parallel to each other, interaction is
> expected to be repulsive, even though they have opposite charges. Also mind
> that overall structure in such complex systems depends on many different
> interactions, so these two groups are not necessarily close because they
> have interacted favorably, but because the overall interactions within the
> whole system eventually led these groups to approach each other, just like
> groups bearing the same charge pack together in micelles, membranes and
> films, with large repulsive interactions between the charged heads
> (stabilization comes from ionic and dipolar screening along with
> hydrophobic interactions).
> On Wed, May 27, 2015 at 3:09 AM, Raj D <gromacs.for.f at gmail.com> wrote:
> > Dear Users,
> > I have just completed simulation of a ligand and enzyme complex and
> > when I visualized the trajectory , I have noted an important close
> > contact say about (7 to 10 A distances) between an active site residue
> > Arg and the carboxylate group of the ligand through out the simulation
> > time of 10ns. I wanted to quantify it using mdrun -rerun option and
> > evaluated energy (COUL-SR) value of the polor atoms of the Arg and
> > carboxylate as energygroup in my mdp file , and surprisingly I found
> > the values are big positive numbers whereas I expected a negative
> > values. Why the contradiction happens , trajectory showed attraction
> > and energy is dispersion ?
> > I just pasted few lines of the energy.xvg
> > @ s0 legend "Coul-SR:Arg262_NH-CPG_COOH"
> > @ s1 legend "Coul-14:Arg262_NH-CPG_COOH"
> > 0.000000 5.647315 0.000000
> > 2.000000 5.367461 0.000000
> > 4.000000 6.109462 0.000000
> > 6.000000 0.976809 0.000000
> > 8.000000 4.306820 0.000000
> > 10.000000 2.926659 0.000000
> > 12.000000 2.567632 0.000000
> > 14.000000 1.934579 0.000000
> > 16.000000 3.874691 0.000000
> > 18.000000 3.130555 0.000000
> > 20.000000 1.804790 0.000000
> > expecting you experts opinion on this.
> > Regards,
> > Raja
> > --
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> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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