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
