Couple of methods come to mind: # cut the box into slices, small enough so that angle between the tube axis and line to the AA has little effect on the distance. Then do COM to AA analysis in each slice, then "add" the slice results together. This is an approximation. # align tube axis along one of the axes, then measure the distance components, then calculate from the appropriate x,y,z pair of terms. If correctly align, this will be most accurate.
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Sat, 27 Oct 2018 at 23:03, rose rahmani <rose.rhm...@gmail.com> wrote: > > Hi, > > I want to calculate distances between fixed tube in the middle of the box > and amino acids(all are same type)around it. But gmx distance gives me the > relative distance i mean AA can be front or back( can be 0.5 or -0.5 from > tube) of tube but still |-0.5|=0.5 nm far from it. How can i have the > absolute value of distances? > Would you please help me? > > Best > Rose > -- > 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.