Thank you very much, Justin! I tried this command:
gmx_seq analyze -f numcont.xvg -dist num_dist.xvg and I got a histogram. Now the number of contacts between the ion and the polymer is between 160-180. I just want to be sure if I am doing this analysis correct. When I use gmx mindist, from the index file I choose a group of the ion (including 46 ions) and then the polymer group (all polymer chains in the box). I think maybe instead of choosing all ions, I should only select one of them and get the number of contact with the polymers but then since I have 46 of this ion in the simulation box, can it be a good representative of the whole system? If not, what else can I do in this case? Besides, it is mentioned in the Gromacs manual, that if we use the -group option a contact of an atom in another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. I want to count all contact with a polymer chain as 1 contact and check the number of contacts with different polymer chains so by using -group and having the ion as the first group and polymer as the second group from the index file, can I get this? The last question, can I do the same approach to get the distribution of coordination number for the first coordination shell of ions and special atoms of the polymers? Best regards, Mahsa On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/17/19 7:21 AM, Mahsa wrote: > > Dear Gromacs users, > > > > I want to get histograms of the number of polymer-ion contacts average > > across the simulation. For this I used, > > > > gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od > mindist.xvg > > -on numcont.xvg -or mindistres.xvg -group > > > > and from the index file, I chose the ion first and then the polymer > group. > > The generated file numcont.xvg which is more related to what I am looking > > for, gives number of contacts vs time. How can I get the information > which > > I look for from this analysis? > > Post-process with gmx analyze -dist > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.