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

[折晓会]

Thank you professor Justin! I appreciate your help.

> Date: Wed, 5 Aug 2015 20:47:22 -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 8/5/15 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.
> 
> -Justin
> 
> > 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
> >>
> >> --
> >> ==================================================
> >>
> >> 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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