[gmx-users] RMSF reference state?

[Tsjerk Wassenaar]

Hi Pan Wu,

There are two things to distinguish:

1. The reference structure used to remove translational and rotational
degrees of freedom
2. The reference against which the deviations (on a per atom base) are
calculated that are then squared, averaged and taken the root of (root
mean square fluctuation).

These two need not be the same. It is common, and most sensible, to
calculate the deviations against the average structure, after fitting
all structures in the trajectory against a certain reference
structure. With option -od the deviations against the reference used
for fitting are calculated rather than against the average. You do
need a reference for fitting, since otherwise you include overall
rotation and translation in the calculation of the RMSF, which you
usually wouldn't want.

I hope this makes it clear.

Cheers,

Tsjerk

On Wed, Oct 14, 2009 at 9:12 PM, Pan Wu <pan.wu at duke.edu> 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?
> 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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-- 
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