Re: [gmx-users] how to obtain error bar for plotting?
Hey :) Just some side notes. Make sure to distinguish between 'statistical error' or 'standard error of the mean', which is a measure of how 'correct' your estimate of the average is, and the standard deviation or the variance, which is a measure of the natural spread. The latter is not an error! In addition, there are correlations that make it difficult to assess the standard error of the mean. These correlations can be time correlations, which cause a false decrease of the standard error. But simulations that start from similar starting points are also correlated. If the simulations are too short, and 1 ns seems quite short, then the observations will not be statistically independent, and the standard error will again turn out smaller than it should. Cheers, Tsjerk On Thu, Dec 29, 2011 at 2:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/12/11, leila karami karami.lei...@gmail.com wrote: Dear Mark can I obtain error bar twice the standard error of the average If you've used g_energy -av on multiple sets of data, then it will plot error bars corresponding to various quantities. Since twice the standard error isn't an option it supports (as you know from reading g_energy -h) then you'll have the option of accepting one it does support or looking at the output file with error bars of (say) one standard error and post-processing to double the size. distance between the donor atom of protein and acceptor atom of dna over 1 simulation? You've made one observation from one simulation, so there is no statistical error to report. should I do several simulation. Is 1 simulation enough? Very likely you should do several simulations each much longer than 1ns. You should also examine the literature for people who've tried to observe similar things on similar systems to use their approach as a guide for your own. Mark -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to obtain error bar for plotting?
On 28/12/2011 6:59 PM, leila karami wrote: Dear Mark thanks for your reply. I have a general questions: For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg?// //*** What quantity do you wish to show with an error bar? I want to show output from g_dist with an error bar. That's not a quantity. You need to be able to say something like I want to show with an error bar twice the standard error of the average distance between the terminal alpha-carbon atoms over my five simulations. Once you can do that you can start to construct commands with g_dist and g_analyze to achieve it. Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to obtain error bar for plotting?
On 28/12/2011 6:47 PM, leila karami wrote: Dear all For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg? Can I use above tool for obtaining error bars for a *.xvg file resulting from g_dist? I want to obtain a file (containing error bar) to plot with excel. What quantity do you wish to show with an error bar? Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to obtain error bar for plotting?
On 12/24/2011 10:40 PM, leila karami wrote: Dear gromacs users I would like to calculate the standard deviation (as the error bar) for rmsd.xvg file. If rmsd.xvg was used in excel software, it gives a graph as rmsd vs time. I want to have a file containing rmsd vs time and error bar relating to rmsd values such that after plotting by excel it give rmsd vs time and error bar. The RMS deviation in atomic coordinates between a reference and other state is an exact quantity. There's no statistical error to plot. Mark I have tried using g_analyze: In this tool, is -av mandatory? g_analyze -av average.xvg -errbar stddev -f rmsd.xvg It gives me only a average.xvg file and at the end std. dev. relative deviation of standard -cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS13.215937e-01 5.472631e-02 7.739468e-04 -0.2960.083 how to access error bar values? any help will highly appreciated. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
