Hello all, I m performing a pulling simulation on my Protein-Mg-GTP complex. I have considered pulling between the GTP and a residue of protein. The pull code in the .mdp file im using is as follows:
; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = GTP pull_group1 = Residue pull_rate1 = -0.00005 ; 0.00005 nm per ps = .05 nm per ns pull_k1 = 10000 ; kJ mol^-1 nm^-2 The initial distance between GTP and the residue was 7 A and the desired one was 3A. After the completion of run (10ns), I could get a trajectory where the final distance was still 4.25 A. I tried to continue the simulation for another 10ns with the same value for pull_k1 parameter and one by increasing the value to 100,000 also. In both of the case, the trajectories showed the distance stabilized near _4.25 A only. Can anyone please tell me the reason behind it? What should I do, so that I could get the desired distance ? Any suggestion and help is welcome !!! Thanks, Neeru Sharma -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
