[gmx-users] RMSD for specified length of DNA aptamer

Quyen Vu vuqv.phys at gmail.com
Sat May 25 15:27:25 CEST 2019

You should create an index file (use gmx make_ndx) that contains a list of
the atom you want to perform RMSD calculation on, e.g P atoms, or whatever
you want.
Then when you run gmx rms, you have to pass the index file from the above

On Sat, May 25, 2019 at 11:41 AM mmousivand93 <mmousivand93 at ut.ac.ir> wrote:

> Dear all
> I have been run molecular dynamic simulation between DNA(50bp)and small
> ligand,how to calculate RMSD value for
> specified length of DNA during 50ns simulation(for example  residues
> from 12 to 25)?
> Best Regards
> --
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