I am little confued to use the gmx distance command specifically for my purpose mentioned in my question ;
gmx distance -f file.xtc -s file.gro -n file.ndx for outputting the distance between protein 1 and protein 2, protein 1 and protein 3 , protein 1 and protein 4 I will use -oav or -oxyz or -oall option ?and how can I calculate the distance between the proteins with center of mass of my selection which I am providing though index file? On Tue, Jan 5, 2016 at 5:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/5/16 1:18 AM, Life Sciences Inc wrote: > >> Dear Gromacs Users >> >> Kindly let me know how to calculate the protein protein distance as a >> function of time with gromacs. I want to calculate the distance based on >> the center of mass of the selection which is CA atoms. I have 4 proteins >> in >> the system and want to calculate the distances as distance between Protein >> 1 and Protein 2, then Protein 1 and Protein 3 , then Protein 1 and Protein >> 4. >> >> >> I used gmx mindist command but it cannot be used to calculate distance >> with >> center of mass, I tried gmx distance also, but do not know how to use it >> for my above mentioned purpose. >> >> > gmx distance is the correct command, but you haven't told us what you've > tried and why it didn't work (or why you think it didn't work), so it's not > productive for us to simply guess. > > -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.