First thing is that GROMACS measures things in nanometers, whereas VMD uses Angstroms.
Other thing to check is whether the first and last atom in the index group selected when using polystat is the same as the two atoms you selected in VMD. 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 Tue, 8 Oct 2019 at 02:21, Aishwarya Dhar <dhar.aishwa...@gmail.com> wrote: > Hi > I am trying to calculate the shape of an aggregate which is cylindrical in > shape. > I have used the command > gmx polystat -f aggregate.pdb -s aggregate.tpr -o poly.xvg > > The eigen values from gmx polystat of the aggregate for a particular > frame are 3.3566 0.8837 0.7660 but using VMD the distance between the > extreme ends of the rods are 114.1 29.5 27.8 in that particular frame > Could you tell me what am I missing? > > Thank you > > AIshwarya > -- > 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.