Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the protein rotation, it does not rotate over the time. There are just some localized changes in it. 3)Regarding the distance measurement, I am measuring the distance between the specific atoms of the residue and the atoms of the GTP. Till now, these distances as well as the overall protein geometry is maintained well in the range too. 4)If this kind of pulling does not work out in my case, I will again try it with using "position" geometry too with pull_vec1.
Can you suggest why have I not reached the final distance at the end of the simulation? Is it because of the geometry that I have used, because the force constant is already too high in this case? Thanks again for your response. -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999399.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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