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

[Mark Abraham]

On Nov 22, 2013 5:58 PM, "rajat desikan" <rajatdesikan at gmail.com> wrote:
>
> 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)?

Yup, but is this more important than the alternative problem?

> Will the long range
> corrections/DispCorr correct for this?

Good question, I don't know. Would be easy to do two single-points and
compare the energies and forces.

> 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?

I don't know the work to which you refer, but the point in MD is that one
does not even need to compute the energy every step (and GROMACS does not,
unless nstcalcenergy is 1). Evolution proceeds via the forces. However,
certain algorithms do have ways for energies to affect the sampling, or
perhaps post hoc through reweighting algorithms. Whether the jitter in VDW
energies as particles move across an unswitched VDW cutoff is significant
for these is another matter.

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

The LJ? Not at all ;-)

Mark


> 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
> > > --
> > > Gromacs Users mailing list
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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
> --
> Gromacs Users mailing list
>
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