the program actually reads all frames, but it computes the correlation up to half of the total length of the data (it is a homoscedasticity issue, you should read some textbook on time series analysis before you increase the output length using -acflen)
best André On Thu, Feb 24, 2011 at 5:04 PM, Justin A. Lemkul <[email protected]> wrote: > > > Nilesh Dhumal wrote: >> >> How can I make prog. to read all frames. >> >> > > I already answered this. Use a proper setting for -acflen. > > -Justin > >> On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote: >> >>> Nilesh Dhumal wrote: >>> >>>> Hello, >>>> I am calculating dipole autocorrelation function for my system. >>>> >>>> >>>> I run the simulation for 500ps and the plot of dipole autocorrelation >>>> function shows the results for 250 ps. >>>> >>>> I used the following command >>>> >>>> >>>> g_dipoles -f water.trr -s water.tpr -c -corr total >>>> >>>> Can anyone tell whats the problem. >>>> >>>> >>> This is the expected behavior. See g_dipoles -h, especially the -acflen >>> flag. >>> >>> -Justin >>> >>> >>>> I am using Gromacs VERSION 4.0.7 version. >>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> NIlesh >>>> >>>> >>>> >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> 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 [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 >>> >>> >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [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
