[gmx-users] Misunderstandings with g_rms

Jochen Hub jhub at gwdg.de
Fri Nov 7 13:13:50 CET 2008

DimitryASuplatov wrote:
> Hello,
> I am sorry for this stupid question.
> Lets say I have an index file of all chain A atoms. I want to calculate
> RMS of chain A _backbone_ only.
> I run g_rms. It asks two questions:
> 1/ Select group for least squares fit
> 2/ Select group for RMSD calculation
> To the best of my understanding, I should answer "BACKBONE" to the first
> question and enter group number corresponding to chain A index file to
> the second one.

In your case you need to make an index file with a group of the backbone
of chain a, do something like

make_ndx -f x.gro
chain a
"ChA" & Backbone

then run g_rms with -n

And give the ChainA-backbone group twice to g_rms.

Best, Jochen

> Is that correct?
> Thank you. 
> SDA 
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Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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