Hello, I tried to do COM-pulling simulation (using Gromacs 5 .0.4) to pull a molecule away from sodium ion that is bound to acidic site of protein. My reference group is protein backbone. I do that in presence of solvent. The main problem is that my pulled group is not pulled in linear fashion, it rotates around the solvent droplet so when it is being pulled it shuffle around in different directions. This happens even if I changed the pull-geometry to direction using a vector. Also, I tried to change the pull -dimension from YYY to NNY and the movement was not in z- direction. The only way I can get rid of that rotation or shuffling around is do my pulling without solvent and I need to see the pulling effect in the presence of solvent. I wonder if there is a possibility that my reference group is moving in the solvent and so the spring moves with it,although the reference is supposed to be fixed.
Can anyone help me in that? Any suggestions will be appreciated title = Umbrella pulling simulation define = -DPOSRES_Protein ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250000 ; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from md run ; Single-range cutoff scheme nstlist = 50 ns_type = simple cutoff-scheme = verlet comm_mode = linear coulombtype = cut-off vdwtype = cut-off rlist = 333.3 rcoulomb = 333.3 rvdw = 333.3 Tcoupl = nose-hoover ref_t = 370 tau_t = 0.5 tc-grps = system nsttcouple = 1 ;Pressure coupling Pcoupl = NO ;Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = Y Y Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = X ;its is called like that in index file pull_group2_name = Backbone pull_coord1_groups = 1 2 pull_coord1_rate = 0.02 ; pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 Thanks alot Best Regards, Haidy Metwally PhD. Candidate -- 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.
