Hi Lin, Fair questions.
Worst case: imagine a straight path from A to B, chopped into n=10 stretches d: A----------B Something goes from A to B linearly and you make a hundred observations of the position, ten at each stretch. For each stretch i, the average position is i*d-d/2 and the fluctuation is calculated about that position, but only includes deviations between -d/2 and +d/2. The total fluctuation is around (A+B)/2, and includes deviations with sizes up to +/- (B-A)/2. No surprise that the total RMSF in this case is far larger than the per bin RMSF. In this example the RMSF values would end up similar for each bin. If there are some obstacles along the way, the motion won't be uniform and there will be differences between bins, but as long as there's a trend going from A to B (non-equilibrium situation), the total RMSF will be larger than the RMSF per bin. Hope this answers your questions. Cheers, Tsjerk ---------- Forwarded message ---------- From: Chih-Ying Lin <[email protected]> Date: Thu, Oct 28, 2010 at 8:28 AM Subject: RMSF => still confused ? To: Tsjerk Wassenaar <[email protected]> Hi Tsjerk: Well.... i am still confused about the RMSF. 1. Consider a particle, it has been observed appearing at 100 positions. We have ten observations for one time zone. It took the duration of 10 time zones to get 100 positions 2. The reference position is at the origin. (0,0,0) 3. For each time zones (10 positions), we calculate its standard deviation. => Then, I can get 10 different standard deviations for 10 time zones, SD1, SD2, SD3....... SD10 4. Further, consider the 10 time zone as a big-whole time zone. I calculate the standard deviation for the 100 positions, say SD-whole. 5. Then I found SD-whole > SD1, SD-whole > SD2 SD-whole > SD3 SD-whole > SD4 SD-whole > SD5 SD-whole > SD6 SD-whole > SD7 SD-whole > SD8 SD-whole > SD9 SD-whole > SD10 6. I suppose that min(SD1~SD10) <= SD-whole <= max(SD1~SD10) ? As you said, "the mean squared deviation of the path from A to B around (A+B)/2," 7. Finally, I test the md-results downloading from your website. the full set of results http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ THere are 4000 ps. For every 400 ps, I calculate RMSF. Also, I calculate RMSF(from 0 to 4000 ps) as whole, I found the same thing that For each alpha-carbon, SD-whole > SD1, SD-whole > SD2 SD-whole > SD3 SD-whole > SD4 SD-whole > SD5 SD-whole > SD6 SD-whole > SD7 SD-whole > SD8 SD-whole > SD9 SD-whole > SD10 WHY ??? THank you Lin Hi, Lin, please think your questions over thoroughly in stead of flushing every thought right to the mailing list. It also helps to stick to a certain subject (reply) to make sure everything ends up in the same thread. Maybe it's not a bad idea to read over http://www.catb.org/esr/faqs/smart-questions.html (again). Anyway, this question's quite valid :), and Marks answer is a bit off... The reference structure for computing the RMSF is only used for fitting; you'd also have seen this behaviour if you'd taken an average structure from an equilibrium simulation. The fluctuations are around the mean structure. The larger "fluctuations" in the first part of the simulation are caused by the relaxation from the starting structure. <oversimplification>If you think of the starting structure and the 'equilibrium structure' as position A and B, then the first part shows you the mean squared deviation of the path from A to B around (A+B)/2, whereas the next parts give you the mean squared deviation around B</oversimplification>. Note that this gives you a means to assess whether you've reached equilibrium, albeit not a sufficient measure. Hope it helps, Tsjerk On Tue, Oct 26, 2010 at 8:24 AM, Mark Abraham <[email protected]> wrote: > If the reference structure from which the fluctuations are measured is taken > from the -s file (check the documentation or code), then a non-equilibrium > trajectory could well have this property w.r.t. a crystal structure. > > Mark > > ----- Original Message ----- > From: Chih-Ying Lin <[email protected]> > Date: Tuesday, October 26, 2010 15:55 > Subject: [gmx-users] g_rmsf => average over # of time frames ??? > To: [email protected] > >> >> >> Hi >> >> From source code => gmx_rmsf.c > >> "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ", > >> "deviation) of atomic positions ", > >> > >> if (devfn) { > >> /* Calculate RMS Deviation */ > >> for(i=0;(i<isize);i++) { > >> aid = index[i]; > >> for(d=0;(d<DIM);d++) { > >> rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]); > >> } > >> } > >> } > >> count += 1.0; > >> > >> rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count; > >> > >> > >> Therefore, g_rmsf is the average of structure deviation over the time >> frames. > >> > >> However, I issued the commands ( C-alpha is selected ) > >> g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg > >> g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o >> RMSF-abc-100th-200th.xvg > >> g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o >> RMSF-abc-200th-300th.xvg > >> g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o >> RMSF-abc-300th-400th.xvg > >> g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o >> RMSF-abc-400th-500th.xvg > >> g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o >> RMSF-abc-500th-600th.xvg > >> g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o >> RMSF-abc-600th-700th.xvg > >> g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o >> RMSF-abc-700th-800th.xvg > >> g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o >> RMSF-abc-800th-900th.xvg > >> g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o >> RMSF-abc-900th-1000th.xvg > >> > >> > >> Also, ( C-alpha is selected ) > >> g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o >> RMSF-abc-0th-1000th.xvg > >> > >> > >> > >> Then I ploted, > >> RMSF-abc-0th-100th.xvg > >> RMSF-abc-100th-200th.xvg > >> RMSF-abc-200th-300th.xvg > >> RMSF-abc-300th-400th.xvg > >> RMSF-abc-400th-500th.xvg > >> RMSF-abc-500th-600th.xvg > >> RMSF-abc-600th-700th.xvg > >> RMSF-abc-700th-800th.xvg > >> RMSF-abc-800th-900th.xvg > >> RMSF-abc-900th-1000th.xvg > >> > >> > >> Also, I ploted > >> RMSF-abc-0th-1000th.xvg > >> > >> > >> > >> The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than >> those from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg >> / RMSF-abc-200th-300th.xvg / ...... / RMSF-abc-900th-1000th.xvg....... > >> > >> > >> It does not make sense... I supposed..... > >> Did I misunderstand something ? > >> > >> > >> > >> THank you > >> Lin > >> > >> > >> > >> > >> > >> > >> > >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
