You switched on the position restraint in your mdp file, is that the reason?
________________________________ From: Albert <[email protected]> To: gromacs maillist <[email protected]> Sent: Sunday, 7 April 2013, 2:47 Subject: [gmx-users] fail to pull 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? thank you very much best Albert -- 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 -- 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
