Thank you Dr Andre and Dr Mark for your valuable comments. Regards, Raja On May 27, 2015 6:41 PM, "Mark Abraham" <mark.j.abra...@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 <mo...@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.fo...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.