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

[Johnny Lu]

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


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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