Hi Xavier, I am extremely sorry for incomplete information. But this is a follow up to my previous two emails. Unfortunately I havent received any suggestions for them and it appears like you too missed them. For more clarity I am pasting them here again:
Dear users, To calculate the rotational auto correlation functions, the command mentioned in the maual is: g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit what are the -nparm and -fa options are meant for ? Also do we need to use -fitfn option to obtain the rotational auto correlation functions ?? Ram. Dear users, I have given a command like the following to calculate the rotational auto correlation function: g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b 0000 -e 10000 -n .ndx -d I want to use the second order Legendre polynomial to fit. I integrated the resulting .xvg file, to obtain the correlation time using: g_analyze -f .xvg -integrate The output is the following. Could some one help me in understanding it betterly. Calculating the integral using the trapezium rule Integral 1 120.92840 +/- 0.00000 std. dev. relative deviation of standard --------- cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 2.428352e-02 2.972849e-02 4.204243e-04 9.301 120.228 Which value corresponds to correlation time and in which units (its in ps I suppose) ? Thanks in advance. Ram. On Thu, Sep 4, 2008 at 2:32 AM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Wed, 3 Sep 2008 23:40:14 -0400 > "rams rams" <[EMAIL PROTECTED]> wrote: > >> Hi, >> >> I am so surprised for not finding any one who have better experience with >> g_rotacf. I have been playing around with it and the time correlation >> value >> I got by g_rotacf is so small in comparison to the time correlation value >> I >> calcualted using the hydrodynamic radius of the protein. The value is >> nearly >> 10 times less. Can some one give me a better idea about g_rotacf. >> > Many people have certainly used g_rotacf to get ACFs of different > observables. > > Anyways the way you describe your system, command line and your problem > does > does not help anyone to help you. Read your message above and think about > what > you would answer! You've played around with g_rotacf therefore you know it > is not straightforward to give you the magic command. > > XAvier. > >> >> Ram. >> > > ----------------------------------------------------- > XAvier Periole - PhD > > Molecular Dynamics Group / NMR and Computation > University of Groningen > The Netherlands > ----------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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