On Sat, Apr 6, 2013 at 2:47 PM, Albert <[email protected]> wrote: > Dear: > > I am trying to pull my ligand outside of the binding pocket with > following configurations: > > title = Umbrella pulling simulation > define = -DPOSRES > ; Pull code > pull = umbrella > pull_geometry = distance ; simple distance increase > pull_dim = Y N N > pull_start = yes ; define initial COM distance > 0 > pull_ngroups = 1 > pull_group0 = Protein > pull_group1 = LIG > pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > > Tcoupl = v-rescale > tc_grps = Protein_LIG Water_and_ions > tau_t = 0.5 0.5 > ref_t = 310 310 > ; Pressure coupling is on > Pcoupl = Parrinello-Rahman > pcoupltype = isotropic > tau_p = 1.0 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 1.0 > refcoord_scaling = com > ; Generate velocities is off > gen_vel = no > ; Periodic boundary conditions are on in all directions > pbc = xyz > ; Long-range dispersion correction > DispCorr = EnerPres > > > > It is quite strange, the ligand is still in place and not outside the > pocket at the end of simulations. I am just wondering where is the problem? > > Hard to tell. Does your ligand have a suitable exit pathway exactly aligned along the x-axis? Have you tried increasing the pull rate? How long is the simulation? I don't even see nsteps in the above .mdp file. How about increasing the force constant? Is the vector connecting the COM of the entire protein and the COM of the ligand suitable for describing the exit pathway?
-Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
