Hi Justin Bouncing back on your early answer about gmx distance, I noticed something strange (to me)
I'musing the same instruction for a protein file prot.gro gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" and now I'm running umbrella sampling with pull code starting from prot.gro pulling groups are the same 'Protein' and 'Ligand' and strange the first line in the pullx.xvg file does not give the same distance as gmx distance !! Any idea why ? Thx -----Message d'origine----- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Justin Lemkul Envoyé : jeudi 2 mars 2017 23:12 À : gmx-us...@gromacs.org Objet : Re: [gmx-users] Distance between centers of mass On 3/2/17 4:15 PM, ÁLVARO RODRIGO RUIZ FERNÁNDEZ wrote: > Dear GROMACS users: > > How can I calculate the distance between centers of mass of two > residues in time with gmx distance?, I do not understand the sentence > "com of resname AAA plus com of resname BBB" from the manual, pag 241 . > Thanks. > > This is simply the selection syntax for doing exactly what you describe. You can select by residue name, number, etc. or by an existing index group, e.g. gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
