Thank you professor Justin! I appreciate your help. > Date: Wed, 5 Aug 2015 20:47:22 -0400 > From: [email protected] > To: [email protected] > 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: [email protected] > >> To: [email protected] > >> 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 > >> > >> [email protected] | (410) 706-7441 > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> ================================================== > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > >> a mail to [email protected]. > > > > > > -- > ================================================== > > 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 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
