[gmx-users] Diffusion/PBC

[Debashis Sahu]

Thanks Thomas for your suggestion......it looks fine.


On Wed, Nov 6, 2013 at 10:00 AM, Trayder Thomas
<trayder.thomas at monash.edu>wrote:

> 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.*
> > > --
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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-- 
*Debashis Sahu*
*Central Salt and Marine Chemical Research Institute*
*Bhavnagar, Gujarat*
*India, 364002.*