Pan Wu wrote:
Yes, I also think the *.tpr after -s maybe the reference state. However,
In this way, why in the manual it says like this?
"With the option -od the root mean square deviation with respect to
the reference structure is calculated"
What about without -od, should there be no reference structure or the
reference structure is taken as average over the trajectory?
You're talking about two separate calculations. Using -od calculates some sort
of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using
the fitting described (unless you use -nofit).
-Justin
Thanks!
Pan Wu wrote:
> Hi everyone,
> Thank you for answering my former questions, it really help me, the
> new gmx-er a lot~
> Here is another question about reference state of RMSF.
> In the manual, it shows "g_rmsf computes the root mean square
> fluctuation (RMSF, i.e. standard deviation) of atomic positions
> after (optionally) fitting to a reference frame". So in this way, can I
> choose the reference frame from *.tpr file or the coordinate average
> over the whole trajectory? If Gromacs can, how?
I believe the reference structure is taken from whatever structure file
is given
to the -s flag, so in principle you could provide any frame from the
trajectory,
as well as the initial one, or some average structure (from, i.e.
g_cluster or
something similar).
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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