[gmx-users] Nstlist and constrain simulations

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 1 19:28:15 CET 2016


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?"

> 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 ;-)

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.

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?


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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