[gmx-users] Error:EM did not converge while using polarizable ion
Vitaly V. Chaban
vvchaban at gmail.com
Tue Aug 4 17:10:11 CEST 2015
The largest force suggests that some atom somehow gets onto another
atom. Looking at the topology file is necessary to issue further
I am not sure that Fmax < 1 (which units?) is an adequate criterion...
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).
>> 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 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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