[gmx-users] RMSF reference state?

Pan Wu pan.wu at duke.edu
Wed Oct 14 21:12:04 CEST 2009

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
What about without -od, should there be no reference structure or the
reference structure is taken as average over the trajectory?


>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
>to the -s flag, so in principle you could provide any frame from the
>as well as the initial one, or some average structure (from, i.e. g_cluster
>something similar).
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