In case anybody else finds the gmx distance input as confusing as I did... if you want to get the distance between the center of mass of the peptide and the center of mass of the SDS, you would first create Protein and SDS groups in an index file (say they are groups 1 and 2), then send that to "gmx distance" and you would type "com of group 1 plus com of group 2" interactively or script the piping of this text into "gmx distance"
________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 16 May 2016 07:51:51 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Calculating Distance On 5/16/16 3:20 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > Hello everyone, > I'm simulating a peptide in an SDS micelle. The simulation was > performed for 100ns > When I visualize the trajectory in VMD, the peptide moves to the SDS > interface where initially it was placed in the center, the results > are as expected. I would like to calculate the distance the peptide > has traveled or moved from the center to the interface > > > Any suggestions on how to go about doing this? > Calculating distances is what the gmx distance program is for. Simply obtain the COM distance between the micelle and peptide (or any subset of atoms that makes sense). -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.
