[gmx-users] Diffusion/PBC

[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 <tsjerkw at 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.sahu87 at 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 at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>