[gmx-users] RMSF reference state?

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 14 21:48:07 CEST 2009

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).


> 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).
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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


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