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.