Hi Justin! I try to apply restraint just to the O atom. There is another question about the set of the coulomb and the vdw interaction for the ion-water cluster Na(H2O)_250. My set is shown as follow:
; vdw vdw-type = Cut-off rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field ;cut-off ^M rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)^M epsilon_rf = 2.0 epsilon_r = 0.5 cutoff-scheme = group The radius of the cluster is about 1.12 nm. Is this set appropriate ? Best regards, Yong Liu liuyong_1...@dicp.ac.cn From: Justin Lemkul Date: 2014-11-14 10:40 To: gmx-users Subject: Re: [gmx-users] Flat-bottomed position restraint set On 11/13/14 7:15 PM, liuyong_1...@dicp.ac.cn wrote: > Hi Justin! > I use the geometric center of the sphere as the reference coordinates. > However, there are still water molecules escaping to the vacuum. Is there > other way to aovid this ? > This shouldn't happen if things are set up right. Try applying the restraint just to the O atom, not all 3 atoms of the water individually. We do this routinely and it works quite well. -Justin > Best regards, > Yong Liu > > > > liuyong_1...@dicp.ac.cn > > From: Justin Lemkul > Date: 2014-11-12 21:54 > To: gmx-users > Subject: Re: [gmx-users] Flat-bottomed position restraint set > > > On 11/12/14 8:08 AM, liuyong_1...@dicp.ac.cn wrote: >> Dear Gromacs users! >> >> I use the flat-bottomed position restraints to avoid the molecules to escape >> from the clusters to the vacuum. The parameters of the restraints on water >> molecules are shown as follow: >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct g r(nm) k >> 1 2 1 3 30.0 >> 2 2 1 3 30.0 >> 3 2 1 3 30.0 >> #endif >> However, water molecules still escape away from the cluster to the vacuum >> after about 100 ns MD run at 550K. What should be done with the restraints >> to avoid the water molecules to escape to the vacuum? >> > > Are you using suitable reference coordinates passed to grompp -r? If you're > not, then the reference coordinates are whatever is in grompp -c, which means > your water molecules can deviate up to 3 nm from that position without > penalty. > For a sphere, the reference coordinates for the water should be the > geometric > center of the sphere. > > -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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
