[gmx-users] Coul-SR: positive value for interating group

[Mark Abraham]

Hi,

Indeed. Many force fields in common use are additive, but this is not the
same as decomposable!

Mark

On Wed, May 27, 2015 at 2:52 PM André Farias de Moura <moura at ufscar.br>
wrote:

> Raja,
> 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).
> best
> Andre
>
> 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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