[gmx-users] Change in atom name

Dallas Warren dallas.warren at monash.edu
Fri Oct 5 01:22:28 CEST 2018

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, <
mahdisobatinezhad at 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
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