[gmx-users] Distance issue

[V.V.Chaban]

Hmm. If you exclude PBC manually, do you get a pick when expected?

Professor Vitaly V. Chaban



On Wed, Jul 22, 2015 at 8:10 AM, Navneet Chaturvedi
<14.navneet at gmail.com> wrote:
> Dear Scientists
>
> My system contains Protein+ZN+ions+water. Box size from protein surface is
> 1.0nm. After production MD of 50ns, when I calculate the distance (g_dist)
> from one Zn ions to a particular Amino Acid residue, then I got huge
> distances more than 5nm (even more) somewhere in plot. How it is possible
> the distances more than box size.
>
> I am new in the field, so could anyone make some light on it. Is it PBC
> problem?
>
> Thank you
>
> --
> *Your Sincerely*
>
> *Navaneet Chaturvedi*
> Dr Gali Prag
> Department of Biochemistry & Mol Biology, Sherman Building
> Tel Aviv University, Tel Aviv 69978
> Israel
> Email: navaneettau at post.tau.ac.il
> Contact (Israel): +972 (0) 547387142
>              (India):  +91 9451067728
> Skype: navneetonskype1
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