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

[André Farias de Moura]

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