[gmx-users] RMSD calculation of protein-ligand complex

ashutosh srivastava ashu4487 at gmail.com
Fri Apr 22 11:52:58 CEST 2016

Hi Aswathy

You can make a group with Protein and ligand in an index file using
make_ndx and pass it with -n in gmx rms.


On Fri, Apr 22, 2016 at 6:46 PM, Aswathy soman <aswathyneeharika at gmail.com>

> Hi,
> I have done a 100 ns simulation of protein-ligand complex. I was wondering
> is it possible to calculate RMSD of the entire protein-ligand complex. How
> to select the complex as such during the calculation of RMSD because there
> is no group as protein+ligand. Thanking you in advance
> Regards,
> Aswathy
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