Re: [gmx-users] gmx rmsdist: rmsmax vs. rmscmax
Hi, thanks for the reply. I now have another question regarding the the rmsdist tool: I'm confused why my rmsmax value seems so small. Right now I am simulating a box of water only. I'd like to get a matrix of all the atom-atom distances for a single frame in my simulation, so use the following command: gmx rmsdist -f nvt.trr -s nvt.tpr -mean -nosumh -b 100 -e 100 However, this gives an rmsmax = 0.000345129, which is smaller than a water molecule, and Im not sure why. I'm also curious why I need to supply a topology file if all I want to calculate is the interactomic distances. I'm likely misunderstanding this tool... Thanks in advance for the help. Regards, Alan Manning On 03/16/15 04:24, Justin Lemkul wrote: On 3/15/15 6:36 PM, Alan Manning wrote: Hi What is the difference between the rmsmax and rmscmax values written to the screen when running gmx rmsdist? Thanks. rmscmax is scaled by dividing by the mean (sc for scaled, presumably). See calc_rmsd() in gmx_rmsdist.c -Justin -- 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.
Re: [gmx-users] gmx rmsdist: rmsmax vs. rmscmax
On 3/15/15 6:36 PM, Alan Manning wrote: Hi What is the difference between the rmsmax and rmscmax values written to the screen when running gmx rmsdist? Thanks. rmscmax is scaled by dividing by the mean (sc for scaled, presumably). See calc_rmsd() in gmx_rmsdist.c -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.
[gmx-users] gmx rmsdist: rmsmax vs. rmscmax
Hi What is the difference between the rmsmax and rmscmax values written to the screen when running gmx rmsdist? Thanks. Regards, Alan Manning -- 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.
