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? 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 ; Thank you so much, Hongtham On Sat, May 28, 2016 at 12:10 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/26/16 9:20 PM, HongTham wrote: > >> Dear Gromacs users, >> Im running a Zn bound protein - ligand complex system. Zn makes >> coordinations with 3 HIS and NH- of ligand. in the itp file, Zn and >> protein >> in the same [molecule] but not ligand. because it cant be applied distance >> restraint ZN and ligand (they are belong to different [molecule]), I >> applied distance restraint for ZN and 3 HIS, and used pull code to keep >> ligand closed to ZN >> This is the distance restrains assigment in topology file of ZN and >> protein, while 3852 is ZN and other is HIS atoms. >> [ distance_restraints ] >> ; ai aj type index type low up1 up2 fac >> 3852 1354 1 0 1 0.2 0.21 0.22 0.1 >> 3852 1390 1 0 1 0.2 0.21 0.22 0.1 >> 3852 1721 1 0 1 0.2 0.21 0.22 0.1 >> >> The pull code in mdp file is like below, in which, a_3862 is N atom of >> ligand >> disre = simple ; distance restraints >> disre_fc = 1000 ; Force constant >> pull = umbrella >> pull-ngroups = 2 >> pull-ncoords = 1 >> pull-group1-name = ZN >> pull-group2-name = a_3862 >> pull-geometry = distance ; simple distance increase >> pull-coord1-groups = 1 2 >> pull-dim = Y Y Y >> pull-coord1-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-start = yes ; define initial COM distance > 0 >> pull-nstxout = 5000 >> pull-nstfout = 5000 >> >> >> It seemed the pull code worked well. The problem is the distance restraint >> is not effective. ZN only can be kept closed to one of three HIS, and >> moves >> far away from 2 others. >> > > Because you defined one restraint using the pull code. Either define > multiple restraints or increase the strength of your distance restraints. > > -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.