Hi Tsjerk, Please see the box here https://www.dropbox.com/s/cu70fw2dmwaxl1x/Editconf.png?dl=0.
On Sat, Mar 14, 2015 at 1:38 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Rajan, > > Do you see the box? > From your output it is easily seen that the new center equals > 0.5*boxvectors. > > Cheers, > > Tsjerk > On Mar 14, 2015 5:47 AM, "Rajan Kumar" <kumarrajan...@gmail.com> wrote: > > > Hi all, > > > > I am trying to study wetting of water on Graphene oxide(GO). My > > structure has functional group in form of epoxide group > > on one side of the Graphene sheet. Also I have added water > > molecules in form of spherical droplet on the same side of the sheet. > > > > I used the following commands to generate .gro. > > > > editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c > > > > --------------------------------- > > > > Read 260 atoms > > No velocities found > > system size : 1.845 1.562 1.523 (nm) > > center : 0.985 0.828 0.380 (nm) > > box vectors : 0.000 0.000 0.000 (nm) > > box angles : 0.00 0.00 0.00 (degrees) > > box volume : 0.00 (nm^3) > > shift : 0.515 0.672 1.120 (nm) > > new center : 1.500 1.500 1.500 (nm) > > new box vectors : 3.000 3.000 3.000 (nm) > > new box angles : 90.00 90.00 90.00 (degrees) > > new box volume : 27.00 (nm^3) > > > > > > > ---------------------------------------------------------------------------- > > > > My question is, what is this* center* and how is it calculated by > editconf? > > When I see conf.gro in VMD, I don't actually see my system at the > geometric > > center of the box. > > > > > > > > > > -- > > Rajan Kumar > > Indian Institute of Technology, Guwahati > > > > -- > > 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. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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.