[gmx-users] Distance Issue

[V.V.Chaban]

I mean to exclude PBC from the plot post factum.

If you subtract the box side length from your "huge distances", do you
get trustworthy distances?

Also, i would compute RDF and compare the positions of peaks in the
RDF with what you have in g_distance.




On Wed, Jul 22, 2015 at 9:16 AM, Navneet Chaturvedi
<14.navneet at gmail.com> wrote:
> Respected Dr. Chaban
>
> I did -pbc mol and used the output xtc. Should I use xtc without nojump or
> mol option.
> Thank you for your text.
>
>
>
> Message: 6
> Date: Wed, 22 Jul 2015 09:00:07 -0300
> From: "V.V.Chaban" <vvchaban at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Distance issue
> Message-ID:
>         <CAPXdD+ZOxT8VHi+t-JeePFUmTA0Oh982Krh7eDwO066s5X5Akg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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
>
> --
> 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