[gmx-users] Error:EM did not converge while using polarizable ion

[Justin Lemkul]

On 8/4/15 11:09 AM, Vitaly V. Chaban wrote:
> The largest force suggests that some atom somehow gets onto another
> atom. Looking at the topology file is necessary to issue further
> guesses.
>
> I am not sure that  Fmax < 1 (which units?) is an adequate criterion...
>

kJ mol^-1 nm^-1 like any other force.  A value of 1 is appropriate.

-Justin

>
>
>
>
> On Mon, Aug 3, 2015 at 8:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 8/3/15 6:38 PM, 折晓会 wrote:
>>>
>>> Dear professor Justin,
>>>
>>> Thank you very much for your suggestions! I really appreciate your help!
>>>
>>> I build a larger system and use the parameters you suggested. The
>>> simulation is working better now, especially after decreasing the time step,
>>> but EM occasionally does not converge in some steps during the simulation.
>>> For example,
>>>
>>> step 341262: EM did not converge in 100 iterations, RMS force 2.608
>>> step 341263: EM did not converge in 100 iterations, RMS force 15.730
>>> step 341264: EM did not converge in 100 iterations, RMS force 40.663
>>> step 341265: EM did not converge in 100 iterations, RMS force 88.519
>>> step 341266: EM did not converge in 100 iterations, RMS force 173.432
>>>
>>> step 473594: EM did not converge in 100 iterations, RMS force 9.094
>>> step 473595: EM did not converge in 100 iterations, RMS force 24.042
>>> step 473596: EM did not converge in 100 iterations, RMS force 57.226
>>> step 473597: EM did not converge in 100 iterations, RMS force 127.469
>>> step 473598: EM did not converge in 100 iterations, RMS force 285.591
>>> step 473599: EM did not converge in 100 iterations, RMS force 479.862
>>>
>>> I am wondering if this is common for polarizable model simulations. I
>>> tried to use different time steps (0.2, 0.5 and 0.8 fs) and longer steps
>>> (500 000, 800 000), but the similar warnings occured periodically as above.
>>>
>>> In addition, I am also confused about the outcome of the energy
>>> minimization, since it reaches neither the emtol (1) nor the nsteps (50000):
>>>
>>> Energy minimization has stopped, but the forces have not converged to the
>>> requested precision Fmax < 1 (which may not be possible for your system).
>>> It
>>> stopped because the algorithm tried to make a new step whose size was too
>>> small, or there was no change in the energy since last step.
>>>
>>> Steepest Descents converged to machine precision in 2115 steps,
>>> but did not reach the requested Fmax < 1.
>>> Potential Energy  = -1.0560062e+09
>>> Maximum force     =  1.7716933e+15 on atom 2483
>>> Norm of force     =  4.9991217e+13
>>>
>>> Based on this outcome, is it due to the low machine precision which stops
>>> the energy minimization?
>>>
>>
>> No, there's something catastrophically wrong with your system.  The maximum
>> force is 10^15!  There's no point in doing dynamics with such a system.
>> Either the topology is somehow incorrect or the starting coordinates are
>> unreasonable such that they cannot be fixed with EM.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
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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

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