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

[Raj D]

Thank you Dr Andre and Dr Mark for your valuable comments.
Regards,
Raja
On May 27, 2015 6:41 PM, "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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > _____________
> >
> > Prof. Dr. André Farias de Moura
> > Department of Chemistry
> > Federal University of São Carlos
> > São Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.