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

[Mark Abraham]

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.
> > > --
> > > 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-request at 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-request at 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-request at gromacs.org.
>