[gmx-users] Nstlist and constrain simulations
pall.szilard at gmail.com
Tue Feb 2 15:04:29 CET 2016
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:
>> 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
>>> 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
>> 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
No, it should not; for details see manual section 3.4.2.
What GROMACS version are you using?
> Kind Regards,
>> Thanks in advance.
>>> Kind Regards,
>>> Michail (Michalis) Palaiokostas
>>> PhD Student
>>> School of Engineering and Materials Science
>>> Queen Mary University of London
>>> Gromacs Users mailing list
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users