[gmx-users] RMSF reference state?

[Tsjerk Wassenaar]

Hi,

Actually, Justin is completely right (and I should've checked g_rmsf
-h). -od calculates the RMSD from the structure in the frame against
the structure in the topology file. This does not nullify the
statements regarding references for fitting and references for
deviations though :p

Cheers,

Tsjerk

On Wed, Oct 14, 2009 at 9:48 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623