[gmx-users] Molecule specific explosion

[Justin Lemkul]

On 5/26/15 4:52 PM, Eric Smoll wrote:
> Hi Mark,
>
> Good question. I have rerun the simulation using a single molecule in a box
> without periodic boundary conditions and I see an identical distortion
> during energy minimization. Most of the suggestions present in
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up describe
> instability during MD. I am seeing this extreme geometry distortion much
> earlier during equilibriation.
>

For the purposes of diagnosing something that's crashing, the distinction 
between "equilibration" (which is an MD process) and "MD" is totally irrelevant. 
  Blowing up typically occurs during the earliest stages of whatever the 
simulation is.

Perhaps I'm missing some details, but what is this molecule?  Where did you get 
its parameters?  What chemical groups are distorting, and in what way?  If a 
single molecule in vacuum is crashing, then the topology is absolutely the 
problem.  Posting the topology would be useful.

-Justin

> Best,
> Eric
>
> On Tue, Apr 28, 2015 at 3:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> What happens when you use this topology on a single molecule? Other
>> standard techniques for diagnosing at
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>
>> Mark
>>
>> On Tue, Apr 28, 2015 at 8:09 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
>>
>>> Hi Mark,
>>>
>>> Thanks for the reply. In my previous message, one molecular component of
>> my
>>> liquid solution greatly-deforms ("explodes") on  energy minimization. I
>>> have examined the topology and everything seems in order. No warnings
>> were
>>> generated by grompp or mdrun. Here are my minimization settings:
>>>
>>> constraints=h-bonds
>>> integrator=steep
>>> emtol=1000.0
>>> emstep=0.01
>>> nsteps=10000
>>> nstlist=10
>>> nstxout=1
>>> ns_type=grid
>>> rlist=1.5
>>> coulombtype=PME
>>> rvdw=1.5
>>> rcoulomb=1.5
>>> pbc=xyz
>>> cutoff-scheme=verlet
>>> nstcalclr=1
>>>
>>> The liquid topology file is generated by pdb2gmx using aminoacids and I
>>> detect no errors.
>>>
>>> Best,
>>> Eric
>>>
>>> On Sun, Apr 26, 2015 at 2:08 AM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Look at the whole molecule topology. Don't ignore any warnings.
>>>>
>>>> Mark
>>>> On 26/04/2015 9:38 am, "Eric Smoll" <ericsmoll at gmail.com> wrote:
>>>>
>>>>> Hello Gromacs Users,
>>>>>
>>>>> I have constructed a multi-component solution and, during energy
>>>>> minimization, one molecule type is radically deforming under ~ 0.2
>> ps.
>>>> All
>>>>> molecules of this type "explode" simultaneously. Looking over the
>>>> topology,
>>>>> all the atoms in this molecules appear to have correct forcefield
>>>>> assignments. I am writing to ask if anyone might have a suggestion on
>>>> how I
>>>>> can identify the origin of this problem.
>>>>>
>>>>> Best,
>>>>> Eric
>>>>> --
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-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================