[gmx-users] Coulombic potential modifiers in Gromacs 4.6.4.

[rajat desikan]

Hi Mark,

Thanks for the answer. I have a few doubts.

1) "The whole potential is shifted by the value that it would otherwise
have had at the cut-off." Doesn't this reduce the well-depth/epsilon for
the LJ potential (same artifact as shifted LJ)? Will the long range
corrections/DispCorr correct for this?

2) "This is cosmetic in MD, unless you plan to compute based upon the
energies." I am not very clear on this. Are there situations when I should
not be using this? I can understand that shifted potentials cause
difficulties in sensitive cases like near gas-liquid critical points, etc.
Are there bio-molecular situations that one should be cautious about?

3) How would these modifiers affect the simulation in the presence of an
external electric field?

Thanks, I appreciate your time. The manual did not have the answers I need.


On Fri, Nov 22, 2013 at 10:03 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Nov 21, 2013 9:20 AM, "rajat desikan" <rajatdesikan at gmail.com> wrote:
> >
> > Hi All,
> >
> > I was wondering about the coulomb-modifier = Potential-shift-Verlet
> option
> > in conjunction with the Verlet cut-off scheme and PME.
> >
> > I can understand that vdw-modifier = Potential-shift-Verlet shifts the
> > truncated LJ tail by a constant so that the potential is the integral of
> > the force.
>
> No, see http://manual.gromacs.org/online/mdp_opt.html#el. The whole
> potential is shifted by the value that it would otherwise have had at the
> cut-off. This is cosmetic in MD, unless you plan to compute based upon the
> energies. Whether something else is trying to compensate for the missing
> long-range interactions has nothing to do with it.
>
> Mark
>
> >  What does the coulomb-modifier do? We are accounting for the
> > long range coulombic interactions using reciprocal space sums in PME,
> > right? What exactly is the shift here?
> >
> > Thanks
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore