[gmx-users] Equilibration from Non-shifted to Shifted Potential

[Johnny Lu]

In another mdp file, i specified "vdw-modifier=Potential-shift-Verlet", and
then in the log file, I see the same line "vdw-modifier = Potential-shift",
and I use "cutoff-scheme = Verlet" in all of my simulations.

Since i use rlist=1.3, and verlet-buffer-drift=-1. I guess the line
"vdw-modifier=Potential-shift-Verlet" does nothing different from the
default modifier for me.

Does setting shake-tol affect the simulation, if I use "constraints=none"?

Does setting "ewald_rtol" affect a simulation with "coulombtype = PME" ?

On Fri, Nov 14, 2014 at 10:28 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Fri, Nov 14, 2014 at 3:51 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
> > involved. So shifting the potential would not cause a suddenly impulse on
> > the system.
> >
> > By the way, is Potential-shift the default vdw and coulomb-modifier (so
> > that is used even if i didn't specify a modifier) for gromacs 4.6.7?
> > I didn't see the default value when I searched for vdw-modifier (p.214)
> of
> > gromacs manual 4.6.7, or when I look at the online manual.
> >
> >    coulomb-modifier     = Potential-shift
> >    rcoulomb-switch      = 0
> >    rcoulomb             = 1
> >    vdwtype              = Cut-off
> >    vdw-modifier         = Potential-shift
> >
>
> Indeed, seems we don't document that default (and we should). I forget what
> it is (but it is probably potential-shift-verlet). You can find out what it
> is by commenting those lines out of your input .mdp, and observing what
> grompp fills into the mdout.mdp.
>
> Mark
>
>
> > On Fri, Nov 14, 2014 at 9:31 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Try it and see ;-)
> > >
> > > mdrun -nsteps 10 -reprod -deffnm shifted
> > > mdrun -nsteps 10 -reprod -deffnm not-shifted
> > > gmx check -f shifted -f2 not-shifted
> > > gmx check -e shifted -e2 not-shifted
> > >
> > > Alternatively, given that the forces are not computed from the energies
> > > (e.g. by central difference or some such), what role does the potential
> > > energy play in the integration scheme? :-)
> > >
> > > Mark
> > >
> > >
> > > On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu <johnny.lu128 at gmail.com>
> > wrote:
> > >
> > > > Hi.
> > > >
> > > > If I change my potential from non-shifted to shift, will the sudden
> > > change
> > > > of energy from non-shifted to shifted potential at step 0 completely
> > mess
> > > > up the equilibration?
> > > >
> > > > Thanks again.
> > > > --
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