Jochen Hub wrote:
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
q
then run g_rms with -n
And give the ChainA-backbone group twice to g_rms.
It's not necessarily true that the group used for fitting should be the
group for the RMSD calculation - that's why g_rms allows them to be
different. People should consider their objective and choose
appropriately in each case.
Mark
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