Re: [gmx-users] Diffusion/PBC

2013-11-05 Thread Tsjerk Wassenaar
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.

Re: [gmx-users] Diffusion/PBC

2013-11-05 Thread Trayder Thomas
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

[gmx-users] Diffusion/PBC

2013-11-04 Thread Debashis Sahu
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