Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Would you please let me know how I can get a nice average curve? Also I can see that all of them starting at 1, but I do not think the average is going to 0 finally (my system is 216 spce water, 20ps). Is this because the simulation time is not long enough?? Many Thanks in Advance/Jamie
On Sat, Aug 22, 2009 at 6:49 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jamie Seyed wrote: > >> Hi Justin, >> Thanks for the answer. I want to calculate auto-correlation function of >> R(x,y,z). I mean <R(0).R(t)> , .../Many Thanks in Advance/Jamie >> >> > Coordinates? Use g_traj. > > -Justin > > On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Hi Mark, >> >> Thanks for the answers. I want to use g_analyze but it needs a >> file graph.xvg as an input file. How can I get that for >> calculation of auto-correlation function? Many Thanks in >> Advance/Jamie >> >> >> The graph.xvg file contains the data for which you want to obtain >> the autocorrelation function. Many of the Gromacs analysis tools >> produce .xvg files of whatever quantity they are measuring. I >> suppose it would then be important to figure out what type of data >> you are trying to obtain the autocorrelation function for; that will >> determine which tool to use :) >> >> -Justin >> >> On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham >> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>>> wrote: >> >> Jamie Seyed wrote: >> >> Hi Mark, >> Thanks for the information. Actually in 7.4 I found only >> g_rotacf and >> g_angle also g_sgangle that calculate rotation and angle >> correlation >> function and in appendix D I could not find related >> topic... I >> appreciate if >> someone gives me more detail to do the job. >> I want to calculate <R(0).R(t)> that R is coordinates vector >> R(x,y,z) for >> pure spce water. >> >> >> If that's an auto-correlation function, then g_analyze does >> the job. >> Searching for "correlation" in the manual was a good way to >> start. >> That would also have found a whole section devoted to the topic, >> which is good reading. >> >> >> Also I have a question related to having a coordinate file. >> I >> did a command >> as >> trajconv -f md.trr -n f.ndx -o md.xtc >> I am supposing in this case md.xtc contains only x,y,z >> coordinates. Is that >> true?? Many Thanks in Advance/Jamie >> >> >> Yes, since the compression algorithm used for .xtc only works on >> positions. However it is a lossy compression, and if you want >> full-precision positions-only, look at the options in trjconv >> -h. >> >> >> Mark >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > 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/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/mailing_lists/users.php >
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