Hi James, Thanks for your reply. I roughly got your point and still kinda confused. Please let me know If I am wrong .
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. 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. Well,I am using that pull in each mdp file ( minimization, equilibration and Production). Is that a problem ? It remains nearly at the similar distance as 0th frame throughout the simulations in Z direction. 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. Thanks, Vikas 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? 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