[gmx-users] Nstlist and constrain simulations

Tue Feb 2 15:35:12 CET 2016

On 02/02/16 14:04, Szilárd Páll wrote:
> On Tue, Feb 2, 2016 at 11:17 AM, 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.
>>>> 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
>> problem?
> No, it should not; for details see manual section 3.4.2.
>
> What GROMACS version are you using?

I am using GROMACS 5.1.1

The thing is that I see a difference on the stability when I change
nstlist. In fact it is not crashing when I reduce the nstlist. And to be
honest intuitively it should affect it. Anyway I looked at the manual
but I couldn't see anything directly related to the question posed here.

If as you say, it doesn't affect it, then I am really unaware of the
reason behind the constant LINCS warnings and systems explosion in a
well equilibrated system..

In any case, thank you for your answer.

Kind Regards,
Michail

>> 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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