> suppose distance between center of masses of protein and DPPC is say > 2.5 in > the z direction and if pull_start =yes and pull_init is 1.0 then > sampling > will be at center of mass distance = 3.5 in only Z direction, since I > have > selected N N Y.
That's correct. > > and if pull_start =No and pull_init is 1.0 then sampling will be done > at > center of mass distance = 1 in only Z direction. That's correct. > > Well,I am using that pull in each mdp file ( minimization, > equilibration > and Production). Is that a problem ? That's fine. > It remains nearly at the similar > distance as 0th frame throughout the simulations in Z direction. You may be near an energy barrier if you are sure that you have set the pull settings correctly, so you might have to increase the "spring" constant k in the pull code to get it exactly where you want it. > I am sorry for the misunderstanding. I want to allow my protein only > move > in x, y direction. I am restricting it so It can't move be in Z > direction. There might be other ways to do that with restraints, but this may give you the result you want, too. > > On Wed, Aug 26, 2015 at 8:38 PM, Barnett, James W < > jbarn...@tulane.edu> > wrote: > > > pull_start = yes means COM distance is added to the pull_init > > value. So > > whatever distance your two pull groups starts out at plus pull_init > > is the > > window where it will sample. > > > > pull_start = no means just the pull_init value is used as the > > reference > > distance. If you have pull_init set to 1.0 then that is the > > reference > > distance for sampling (the window where it will sample). > > > > If you haven't equilibrated at the reference distance it could take > > a > > little bit for your two groups to get to the reference distance. At > > t=0 > > nothing has moved yet, unless you have equilibrated with the same > > pull code > > parameters already (and you probably should, depending on what your > > goal is > > here), so you should not expect the distance between the two groups > > to > > already be near the reference distance before the simulation has > > begun. > > > > If you're looking to restrain the protein's movement to the z-axis > > such > > that it can only move along the z-axis, this is not what you'll be > > achieving. Here are you restricting the movement of the protein > > along the > > z-axis but it is free to move in the x and y directions. I may be > > misunderstanding your goal here. There are some flat-bottom > > restraints you > > can add to make it such that the protein only moves in one > > direction if > > that's your goal. Check the relevant sections in the manual. > > > > -- > > James “Wes” Barnett, Ph.D. Candidate > > Louisiana Board of Regents Fellow > > Chemical and Biomolecular Engineering > > > > Tulane University > > 341-B Lindy Boggs Center for Energy and Biotechnology > > 6823 St. Charles Ave > > New Orleans, Louisiana 70118-5674 > > jbarn...@tulane.edu > > > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > > Live King > > <vikasdubey1...@gmail.com> > > Sent: Wednesday, August 26, 2015 5:25 AM > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] Pull parameters to Restrain motion along the Z > > Axis > > > > Hi, > > > > I use Gromacs 4.5.5. I have these pull parameters which I use to > > restrain > > my Protein motion along the Z axis.I want to make sure these > > parameters are > > fine or not since , I am not getting expected results. > > Also, please suggest any other parameters I can add. > > > > ;Pull to restrain Z position > > pull = umbrella > > pull_geometry = distance > > ; Select components for the pull vector. default: Y Y Y > > pull_dim = N N Y > > pull_start = No > > pull_nstxout = 10000 > > pull_nstfout = 10000 > > pull_ngroups = 1 > > pull_group0 = DPPC > > pull_group1 = Protein > > pull_vec1 = 0.0 0.0 0.0 > > pull_init1 = 1.0 > > pull_rate1 = 0 > > pull_k1 = 1000 > > pull_kB1 = 1000 > > > > > > Here I am completely confused in pull_init and pull_start. From my > > understanding, pull_init is the reference distance at t=0. The > > reference > > distance is the distance between COM of the pull group and COM of > > the > > reference group.I have set my reference group as DPPC and pull > > group as > > Protein, which means my Z_distance should be Ideally ~ 1.00 if my > > pull_start is set up as "No" and should be ~0.0 if that is set it > > as > > "Yes".Since, pull_start means the initial COM distance is the > > reference > > distance for the first frame. > > > > But my values are instead after the production run:- > > > > with pull_init =1.0 and pull_start = "Yes" > > time |d| dx > > dy dz > > 0.0000000 4.5361605 0.9850349 2.3691738 3.7407854 > > > > with pull_init =1.0 and pull_start= "No" > > > > 0.0000000 2.8222415 0.7867510 2.5469491 -0.9268878 > > > > > > my protein is nearly at the center of membrane of box size > > > > 7.34147 7.34147 7.34147 > > > > If somebody can help me I will be grateful. > > > > Thanks, > > Vikas > > -- > > 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. > > -- 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.