Re: [gmx-users] Diffusion/PBC
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.comwrote: 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 listgmx-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 listgmx-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
Re: [gmx-users] Diffusion/PBC
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 listgmx-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 listgmx-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 listgmx-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] Diffusion/PBC
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 listgmx-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
