Your best bet is probably to center everything on the receptor. That will prevent jumping of the receptor only, which is hopefully all you need.
-Trayder On Tue, Nov 5, 2013 at 7:14 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Debashis, > > Makes sure that the anion and receptor are together in the reference > structure you use for trjconv -pbc nojump > > Cheers, > > Tsjerk > > > On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu <debashis.sah...@gmail.com > >wrote: > > > Dear All, > > I have an problem related to jumping trajectory. In my MD > > run, there is a receptor molecule which is binding with an halogen anion > in > > water solvent. In the original trajectory, the binding between them looks > > fine but jumping present. To remove the jumping of the system from > > trajectory, I have used 'nojump' as discussed in the forum. Now I got a > > jump-free trajectory, but due to the diffusion here, I have observed that > > the anion and the receptor are far away from each other. I could not fix > > the problem. can any one suggest me? > > Thanks in advance. > > with regards, > > *Debashis Sahu* > > *Central Salt and Marine Chemical Research Institute* > > *Bhavnagar, Gujarat* > > *India, 364002.* > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists