Hi Justin, I got it. Thank you for your explanation. :D Hongtham On Wed, Jun 1, 2016 at 7:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 6/1/16 5:16 AM, HongTham wrote: > >> Hi, >> Im now applying 4 pull codes to keep the Zn coordination. the script is >> like below. >> ; Pull code >> pull = umbrella >> pull-ngroups = 5 >> pull-ncoords = 4 >> pull-group1-name = ZN >> pull-group2-name = a_3862 >> pull-group3-name = a_1354 >> pull-group4-name = a_1390 >> pull-group5-name = a_1721 >> pull-geometry = distance ; simple distance increase >> pull-coord1-groups = 1 2 >> pull-coord2-groups = 1 3 >> pull-coord3-groups = 1 4 >> pull-coord4-groups = 1 5 >> pull-dim = Y Y Y >> pull-coord1-rate = -0.005 ; not pull, just distance restraint at a >> reference distance bw 2 groups >> pull-coord2-rate = 0.0 ; not pull, just distance restraint at a reference >> distance bw 2 groups >> pull-coord3-rate = 0.0 ; not pull, just distance restraint at a reference >> distance bw 2 groups >> pull-coord4-rate = 0.0 ; not pull, just distance restraint at a reference >> distance bw 2 groups >> pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord2-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord3-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord4-k = 1000 ; kJ mol^-1 nm^-2 >> pull-start = yes ; define initial COM distance > 0 >> >> Because the ligand is quite big, so in the initial structure, the distance >> between ZN and ligand is quite big (~ 0.5 nm). my target is to keep the >> distance between Zn and other atom is about 0.2 nm. with The >> pull-coord1-rate=-0.005 nm, i want to quickly pull the ligand to come >> close to Zn. and run NPT which protein backbone restrainted in 1 ns. after >> NPT, now the distance between Zn and ligand is close enough, I will remove >> the pull-rate in the md.mdp. >> the question is, how can I keep the current ZN coordination in MD which a >> specified distance? >> > > A zero pull rate in conjunction with an appropriately specified restraint > distance. > > I added one more option about the referece distance like below. is it right >> for my intention? because the defaut value is 0.0 (at t=0), and I didnt >> specity these value when I run NPT ( the above script), and I thought >> Gromacs assigned the distance from the input structure as the reference >> distance instead of 0. so I am really confused about this option. >> pull-coord1-init= 0.21 ; >> pull-coord2-init= 0.21 ; >> pull-coord3-init= 0.21 ; >> pull-coord4-init= 0.20 ; >> >> > pull-start = yes means "use whatever the distances in the coordinate file > are." > pull-coord*-init = X means "use this value because I'm telling you to." > > > -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.