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 <[email protected]> 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" <[email protected]> > To: gmx-users <[email protected]> > Subject: Re: [gmx-users] Distance issue > Message-ID: > <capxdd+zoxt8vhi+t-jeepfumta0oh982krh7edwo066s5x5...@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 > <[email protected]> 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: [email protected] >> 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: [email protected] > Contact (Israel): +972 (0) 547387142 > (India): +91 9451067728 > Skype: navneetonskype1 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
