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

[André Farias de Moura]

I agree with Mark: pairwise additive potentials are computationally
convenient, but nature does not work like that.

based on your email, it is seems that you are looking for an
energy/enthalpy term explaining some structural pattern, but in most cases
entropy role is also important and in some case might even be the leading
contribution. That being said, you should probably consider some sort of
PMF instead of looking for specific mechanical interactions.

Andre

On Wed, May 27, 2015 at 10:11 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090