Hi Christian, Thank you for your reply. The command worked well. I got the indices of the residues. I want to calculate the occupancies of the residues near my reference ion within say 0.5 nm. It will help me a lot if you could suggest something for it. I have tried gmx distance and gmx mindist with the index file from gmx select, but not successful.
Thanks & Regards, -------------------------- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subho...@yahoo.com On Tue, Feb 18, 2020 at 6:58 PM Christian Blau <b...@kth.se> wrote: > Hi Subhomoi, > > > Yes, > > gmx select > > can do that (see > http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) > <http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html> > > > For what you want to do, it's beneficial to have a look at the selection > syntax here > > http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html > < > http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html?highlight=selection > > > > > Best, > > Christian > > On 2020-02-18 13:14, Subhomoi Borkotoky wrote: > > Hi, > > > > Is there any option in gromacs to list residues/atoms around a reference > > group? I have checked trjorder , but it only gives number of molecules. > > > > Thanks & Regards, > > -------------------------- > > *Subhomoi Borkotoky, Ph. D.* > > Kusuma School of Biological Sciences, > > Indian Institute of Technology Delhi, > > New Delhi-110016, > > India. > > > > Alternate E-mail : subho...@yahoo.com > > > > https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokAAAAJ > -- > 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.