[gmx-users] Nstlist and constrain simulations

[Mark Abraham]

Hi,

On Tue, Feb 2, 2016 at 1:11 PM Michail Palaiokostas Avramidis <
m.palaiokostas at qmul.ac.uk> wrote:

> Hi Mark and thank you for your answer.
> Please see below :)
>
> On 01/02/16 18:28, Mark Abraham wrote:
> > Hi,
> >
> > On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis <
> > m.palaiokostas at qmul.ac.uk> wrote:
> >
> >> Dear GMX users,
> >>
> >>
> >> I would like to ask about your opinion on the size of the neighbour list
> >> (nstlist).
> >>
> >>
> >> I am running constraint simulations
> >
> > What do you mean by a "constraint simulation?"
> Sorry, I should have been clearer. I am using the z-constraint method in
> which I constrain the permeant along the z-axis in various positions and
> I record the constraint force. Similar to umbrella sampling but with
> constrained distances between the permeant and membrane.
>

Using which GROMACS feature? e.g. freeze groups and NPT are usually an
unhappy combination.


> >> of a permeant along a lipid bilayer. In the initial setup the system
> runs
> >> on NPT and nstlist 10 (which GROMACS changes to 40 automatically). With
> >> this setup my simulation is very fast but always crashes at various
> points
> >> with the same way always. Initially it gives some LINCS warnings and
> then
> >> it gives an error that a particle "communicated to PME rank 2 are more
> than
> >> 2/3 times the cut-off out of the domain decomposition cell".
> >>
> > Usually this indicates your setup is unstable e.g. see
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up. I'll
> proceed
> > by assuming you're very confident that your membrane system has had a
> > suitable few dozen+ nanoseconds of equilibration ;-)
> Yes absolutely confident. The system does not crash with unconstrained
> simulations. The membrane-solvent system is well equilibrated for 1μs
> and then, after I introduce the permeant, I perform an energy
> minimization and a short 500ps NPT-Berendsen equilibration to relax the
> pressure that the permeant might have introduced.
>

I'd be skeptical that 500ps was enough.


> > When I see the last pdb steps before crash, sometimes there seem to be
> >> overlaps between the permeants and the lipids and then system explosions
> >> and PBChaos. Other times it is not so dramatic.
> >>
> >>
> >> So the question is, should I be conservative with the nstlist? When I
> run
> >> NPT simulations and change the nstlist to 1, the system does not fail.
> >> Alternatively, if I change to NVT and nstlist to 10, again the system
> runs
> >> successfully. But NVT and 40 crashes.
> >>
> > This might all be a wild goose chase. If you are pulling permeants into
> the
> > membrane, then that creates pressure on the membrane and perhaps
> > destabilizes the pressure coupling. If that's with Parrinello-Rahman then
> > it can easily oscillate out of control, ending up violating the
> assumptions
> > under which the code is written.
> Yes, this is why I run an small equilibration in the beginning. And to
> be honest, technically, I do not pull the permeants. For each position,
> I add it to the system in VMD, and then run the
> minimization-equilibration-production sequence.
> >
> > Since GROMACS was doing the nstlist update automatically, I thought it
> was
> >> a "safe" option. Based on the above,however, I believe that since the
> >> simulation runs with constraints, the system is more sensitive and thus
> the
> >> nstlist should be smaller. Can anyone validate that my hypothesis is
> >> correct?
> >>
> > On the limited evidence available, I think your observations are more
> > likely to be symptoms of the problem than the problem itself. How does
> e.g.
> > one permeant molecule behave?
> Once again sorry for not being clear. The plural in permeants comes from
> the fact that I test several molecules (e.g. water, ammonia etc) but it
> is only one per simulation/system.
>
> So, you think that the updating of neighbour list, shouldn't affect the
> problem?
>

Yep. You can force mdrun to use an nstlist of your choosing with mdrun
-nstlist n. I would expect you to observe similar instability in such
cases. The only case in which I think nstlist could matter is when
something else is so badly wrong that particles diffuse further than the
automated buffer anticipates, in which case any reduction of nstlist that
keeps the simulation running is merely deferring the problem to analysis
time...

Mark


> Kind Regards,
> Michail
>
> > Mark
> >
> > Thanks in advance.
> >>
> >> Kind Regards,
> >>
> >> Michail
> >>
> >>
> >> -------------------------------------------------------------------
> >> Michail (Michalis) Palaiokostas
> >> PhD Student
> >> School of Engineering and Materials Science
> >> Queen Mary University of London
> >> -------------------------------------------------------------------
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