[gmx-users] Diffusion/PBC

[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.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.