[gmx-users] Error:EM did not converge while using polarizable ion
jalemkul at vt.edu
Thu Aug 6 02:47:35 CEST 2015
On 8/5/15 7:43 PM, 折晓会 wrote:
> Thank you professor Justin for the kind help!
> I am wondering if you can provide me some links about hyperpolarization protection since I want to know where the parameters in "POL2" come from. Maybe I missed something, but I did not find corresponding parameters in the SWM4-NDP reference.
There are comments in the force field file itself about what it is and how it is
implemented. Beyond that, see dx.doi.org/10.1021/ct900576a and other associated
Drude papers, particularly those dealing with ions.
> Best wishes,Xiaohui
>> Date: Tue, 4 Aug 2015 19:23:42 -0400
>> From: jalemkul at vt.edu
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Error:EM did not converge while using polarizable ion
>> On 8/4/15 5:40 PM, 折晓会 wrote:
>>> 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:
>> Hyperpolarization protection is often needed in polarizable simulations, so the
>> use of "POL2" in the virtualchemistry.org files makes a big difference. Without
>> this effect, polarization catastrophe is common.
>>> 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.
>> You'll never reach such a tolerance for the whole system using steepest descent
>> in singe precision. That said, the outcome is perfectly reasonable. The value
>> of emtol = 1 in the context of the Drudes/shells is that the maximum allowable
>> force on the Drudes themselves is set to 1 during the run for the purposes of
>> the SCF relaxation.
>> 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
>> Gromacs Users mailing list
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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
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