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

[Johnny Lu]

ewald_rtol affects PME.
http://comments.gmane.org/gmane.science.biology.gromacs.user/50202


On Fri, Nov 14, 2014 at 10:39 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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