VMD colours things based on the atom name. What VMD does has nothing to do with the simulation. To see what is going on, look at the coordinate file (.gro or .pdb)and the atom name, then the topology file (.itp or .top) and the atom names in that. That is what is important, not what a visualisation program does.
On Fri, 5 Oct. 2018, 8:48 am Mahdi Sobati Nezhad, < mahdisobatinez...@gmail.com> wrote: > Hello Gromacs users. > My ligand have two 'Cl' atoms. > I cut atoms from ligand.gro and paste it in complex.gro and then open > complex.gro in VMD and I see that the VMD shows my atoms as Carbon!!! > Do this will not have any effect in my MD?! > > Thanks > -- > 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.
