[gmx-users] Nstlist and constrain simulations

Michail Palaiokostas Avramidis m.palaiokostas at qmul.ac.uk
Tue Feb 2 13:10:43 CET 2016

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.
>> 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.
> 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

Kind Regards,

> 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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