[gmx-users] Nstlist and constrain simulations

Thu Feb 4 17:36:01 CET 2016

Dear Szilárd and Mark,

thank you very much for your help on the issue. I have followed your
suggestions and calculated the total energy and its drift for each of
the test cases I ran. I made a report and uploaded here:
https://drive.google.com/file/d/0B46so7kaQ7F1OW5xd2lzVkcwc2c/view?usp=sharing

In case this is not available in the future, total energy does not
diverge and the drift is negligible and comparable for all cases. The
conclusion is that, as you mentioned, the nstlist did not affect the
total energy conservation. So my system has something else that crashes
it. The question is what and why, but this is another topic. This
question I think can be considered answered. Nstlist does not affect the
stability of constraint simulations.

@Mark
Just for the sake of completion, the method I use to constrain the
distance between the permeant and the bilayer is by using the pull
constrain command. 

Thank you once again for your time.

Kind Regards,
Michail

On 03/02/16 22:05, Szilárd Páll wrote:
> --
> Szilárd
>
>
> On Tue, Feb 2, 2016 at 3:34 PM, Michail Palaiokostas Avramidis
> <m.palaiokostas at qmul.ac.uk> wrote:
>>
>> 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.
> That's if you ignore the automated pair-list buffer estimation.
>
>> Anyway I looked at the manual
>> but I couldn't see anything directly related to the question posed here.
> Perhaps the documentation is not explicit enough about it, but with
> the Verlet scheme implementation, as a pair list buffer is
> automatically determined for the simulated system and setting in
> question (rather than based on a rule of thumb like in the group
> scheme or using an insanely conservative invalidation criteria other
> packages use). Hence, nstlist becomes merely an
> performance-optimization parameter and it won't affect energy
> conservation.
>
>> 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..
> I said *it should not* affect it. The issue is worth investigating,
> though and fortunately, as suggested previously, this is relatively
> easy to verify by simple measurements.
>
> --
> Szilárd
>
>> 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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