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

[折晓会]

Thank you professor Justin and Chaban for helpful suggestions!

In the topology file, I choose "POL2" for water and anions, and the simulation seems working well now. The results of energy minimization are:

Steepest Descents converged to machine precision in 8755 steps,
but did not reach the requested Fmax < 1.
Potential Energy  = -3.0687320e+04
Maximum force     =  1.7012895e+02 on atom 2499
Norm of force     =  7.2500138e+00

Are the results reasonable for the polarizable models? I am wondering why the final force does not match Fmax < 1.

Best wishes,
Xiaohui



> Date: Tue, 4 Aug 2015 11:25:49 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org; vvchaban at gmail.com
> Subject: Re: [gmx-users] Error:EM did not converge while using polarizable ion
> 
> 
> 
> 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
> 
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