[gmx-users] System almost blowing up

Justin Lemkul jalemkul at vt.edu
Tue Apr 4 15:47:54 CEST 2017

On 4/4/17 9:45 AM, Dayhoff, Guy wrote:
>> On 4/4/17 9:31 AM, Dayhoff, Guy wrote:
>>>> On 4/3/17 2:33 PM, Dayhoff, Guy wrote:
>>>>>>> Hi,
>>>>>>> I?m receiving a couple (~15) EM did not converge warnings as well as a few (~3) 1,4 interaction
>>>>>>> warnings during my run. It looks like it starts down the path to blowing up but recovers. Is this ?recovery?
>>>>>>> system dependent? Should I take these messages (even without the subsequent crash) to indicate an
>>>>>>> underlying issue with my system/topology or equilibration? I?m not ignoring or circumventing any warning
>>>>>>> during pdb2gmx, or any other commands.
>>>>>>> For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs emtol of 1.0 and niter of 150
>>>>>>> using the V-rescale thermostat and Berendsen pressure coupling while my systems cell shape relaxes
>>>>>>> as a continuation from position restrained NVT then NPT ensembles. The starting structures were minimized
>>>>>>> in vacuum, then solvated and minimized once again prior to the posres equilibration.
>>>>>> Such a short dt and strict niter should not be necessary in practice.  The
>>>>>> failure of SCF to converge/LINCS warnings is what we typically refer to as
>>>>>> polarization catastrophe, so your system is on the brink of instability.  This
>>>>>> is one of the inherent problems of SCF in polarizable systems; it often fails to
>>>>>> converge and leaves the system potentially unstable.  The reflective hardwall is
>>>>>> much more reliable (and faster).  If the instability is happening in your
>>>>>> equilibration, that may be OK but it is something you should try to troubleshoot
>>>>>> to make sure there's nothing else going wrong.
>>>>>> -Justin
>>>>>> --
>>>>> Got it. I have been spending some time investigating the issue i?m having and
>>>>> after reading shellfc.cpp I was pretty confident the issue was with SCF not converging,
>>>>> and so my niter and dt were an attempt at looking into that.
>>>>> The workflow i?ve been trying to use is?
>>>>> EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 1bar w/ V-rescale tcoupl ->
>>>>> berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl
>>>>> then once my cell shape has reached an equilibrium I finally switch to NH thermostat and PR barostat for
>>>>> the production run.
>>>>> If I switch to employing the hardwall (and the lagrangian dynamics for drudes) then I understand it is not
>>>>> compatible yet with NPT ensembles. So, if I change my work flow as follows would it be appropriate still?
>>>>> EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT semi-isotropic varying pressures
>>>>> w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then switch to NVT without pcoupl
>>>>> to use the hardwall during my production run?
>>>>> For some reason, i?ve got this idea that I need to be tcoupling and pcoupling during my production runs
>>>>> so i?ve been apprehensive to do this.
>>>> If you want an NPT ensemble during dynamics you're going to have to use NAMD,
>>>> CHARMM, or OpenMM.  I haven't coded the barostat yet (fixing the DD bugs has
>>>> been more important).  You can equilibrate with SCF under NPT and get a suitable
>>>> density, then switch to NVT, but your use of semi-isotropic coupling suggests a
>>>> membrane system?  In that case, I would not use NVT during production as you
>>>> will be simulating a constant area, which may not be appropriate.
>>> I?ve parameterized beta-cellulose and then an additional modified form of beta-cellulose for the FF
>>> and i?m looking at the packing behavior of a bundle of strands under the different pressures in water.
>>> Everything seems to be proper apart from encountering the polarization catastrophe randomly,
>>> often times I can restart a downed run and it will move beyond the previous crash point, but this
>>> is tedious and even when I wrote a script to do it for me I found that eventually there was a point
>>> of no return, even if I used the prev_cpt.
>> If you have this many crashes, your physical model is not suitable.  You need to
>> revisit the parametrization before even thinking about more simulations.  An
>> occasional convergence failure with SCF during equilibration is not worrisome,
>> continual problems indicate a bad model.  Your tiny time step and large niter
>> value were clues that this is the case.
>> -Justin
> Okay thanks. To be clear I did use a dt of 1fs and 1.25fs with niter = 50 in my initial runs which all
> went through EM, posres NVT and NPT with scf just fine and then began to have issues after removing
> the posres. Now that i’m writing this I suppose that is also an indication that the issue lies in my parameters
> and the behavior of the strand once it’s allowed to move freely?

Yes, precisely.  If your run only continues if it's restrained or forced through 
by repeated restarts, it's a bad simulation.

For what it's worth, carbohydrate linkages are very complex and we're still 
working on getting all aspects of this right.  It's no surprise you're facing 
issues.  We've been working on disaccharides of all types for months :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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