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.