gromacs does not support "spherical" boxes, as well as I do not think this would have been correct in view of PBC. No PBC will eventually lead to the spherical cluster representation.
On Mon, Dec 7, 2015 at 10:07 AM, mihammad roos <mohammad.roos0...@yahoo.com> wrote: > Hello everybody, > > > > I generated the initial structure by amber tools (the systemis consisted > of a protein with some ions that the whole system is solvated inwater), > then convert the top and crd files to gromacs topology and gro files(by > using parmEd), and then run the equilibration and the production MD > ingromacs. Now I have the trajectory file(.xtc file)( using“gmx trjconv” > command) after running the production MD but I think thereis something > wrong, when I load the xtc file in vmd the protein jump from oneposition to > another position immediately. Actually I put the protein in thecenter when > generating the system. Is it a trouble? > > > I attached an image of the xtc file resulted from runningthe production MD > (using gmx mdrun command notusing gmx trjconv command ), I think the bonds > are not ok, but when loading thextc file resulted from gmx trjconv the > bonds seems good. I don’t if there is aproblem or not > > > By the way I generated another system with a protein and somelipids around > it which is solvated in water by amber tools (the box shape is > spherical),when I convert it to gro and gromacs topology the gro file is ok > (it isspherical) but after running the production MD when I open the > trajectory filethe box is cubic and it is very confused. I want the system > to be spherical. > > > > Thank you, Mohammad. > > -- > 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.
