Hi,
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
step
Best,
On Sat, May 25, 2019 at 11:41 AM mmousivand93
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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