Hi Rodolfo,<br>
<br>
With regards to the first question, the difference is that for the
RMSF, you first determine the average position for each particle and
then calculate the deviation from the average for every time frame,
summing the square of the result and dividing by the number of frames.
When using -od, instead of taking the deviation from the average
position, the deviation from the reference position is taken. In that
case the deviations will be larger in general and the result is heavily
dependent on the choice of the reference. For the most useful results,
use -o rather than -od.<br><br>
The difference between g_rms and g_rmsf is basically that with g_rmsf
you average over time, getting atom or residue specific values, whereas
with g_rms you average over atoms, getting time specific values.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 10/5/05, <b class="gmail_sendername">mekanix</b> <<a href="mailto:mekanix@aruba.it">mekanix@aruba.it</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
And the other question is:<br>I would like to know if the result that g_rmsf -od gives is the same that I<br>will get if I use the time average g_rms per residue<br>Thank's very much to all<br>mekanix writes:<br><br>> Hi Tsjerk, thank you for the answer!
<br>> But my problem is... I can't completely understand<br>> this difference... Maybe rms deviation is a sort of mean value<br>> and rmsf a sort of standard deviation?<br>> Can you explain me in few words the difference?
<br>> Thank's very much<br>> Rodolfo<br>><br>><br>> Hi Rodolfo,<br>><br>> Reading the help (g_rmsf -h) tells that "with the option -od the root mean<br>> square deviation with respect to the reference structure is calculated",
<br>> which is quite different from the root mean square fluctuation of an atom<br>> around its average position, which is what you get with -o.<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On 10/5/05, mekanix <mekanix at
<a href="http://aruba.it">aruba.it</a>> wrote:<br>>><br>>> Hi to all gmx users,<br>>> I'm a new gromax user and I use it for my thesis.<br>>> I have a question for you about the g_rmsf tool...<br>
>> I can't understand which is the difference between<br>>> using the -o and -od options for the outputs file...<br>>> I mean... which kind od results are given by the 2 options<br>>> and which are the dif
<br><br>ferences between them?<br>>><br>>> Another question is: one of those two results is maybe<br>>> the time average of g_rms per residue?<br>>><br>>> Thank's to all<br>>> Rodolfo.<br>
>> _______________________________________________<br>>> gmx-users mailing list<br>>> gmx-users at <a href="http://gromacs.org">gromacs.org</a><br>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a>.<br>>><br>><br>><br>><br>> --<br>><br>> Tsjerk A. Wassenaar, M.Sc.<br>> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>> Dept. of Biophysical Chemistry<br>> University of Groningen
<br>> Nijenborgh 4<br>> 9747AG Groningen, The Netherlands<br>> +31 50 363 4336<br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the www
<br>> interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>