>1. I wonder how I can prove that the core part looks like a sphere? or how >can I measure the Sphericity of the core part? Does Gromacs offer a tool >for that?
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-gyrate.html Then compare rx, ry, rz and/or eccentricity 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 Thu, 8 Nov 2018 at 02:59, Alex <alexanderwie...@gmail.com> wrote: > > Dear all, > I have two types of molecules (molecule number from each 56 and 29 > respectively) in water, the MD simulation gives me a core-shell like system > in which the core part contain one of the molecule type and the shell is > the another one that accumulate around the surface of the core. > > Regarding the system explained above I have below two questions on which > your comments would be highly appreciated; > > 1. I wonder how I can prove that the core part looks like a sphere? or how > can I measure the Sphericity of the core part? Does Gromacs offer a tool > for that? > > 2. If am not wrong the gmx density gives the density only along the X or Y > or Z direction, how I can calculate the density of each of the molecules in > the core-shell system along radius of the sphere , r ? > > Thanks > Alex > P.S. Sorry, do not rely on the spelling auto-correction! :-) > -- > 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.