Hi Justin, Thanks for the answers. Please check below... On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
>> >> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Hi Justin and Mark, >> Thanks. Actually I made a mistake and it seems going to the zero >> (even negative!) >> --But I wanted to know how I can write my command to get only >> one graph (average of all instead of all of them). I read the >> manual chapter-8 and by average I mean I should get one curve >> starting at 1 and coming down to zero...I also tried >> >> >> That's not an average; that's the shape of the ACF curve. >> >> Yes I need to get that shape using g_analyze..!. >> > > Right, I just don't understand why you think you need to obtain some sort > of average. What do you mean by "all of them"? How many graphs are there? Actually when I open autocorr.xvg I can see from data/feature extraction/ the last set is S1295 (N=101, autocorr.xvg) which means they are 1296 graphs each with poor statistics start at 1 and coming down. To have a ACF for a system I expect to get one graph with good statistic... I hope I make it clear now. > > > <snip> > > No, only ACF based on coordinates. I read from the list that people said I >> can use g_rotacf -d for calculation of correlation functions...and actually >> I did it for a simple system. But for new system using another index file it >> is complaining. >> >> > Then I don't think g_rotacf is the tool you want. There is no magic way to > simply calculate some sort of general correlation function. You calculate > an ACF from the specific data you have. So if you're interested in some > sort of position-dependent data, then rotational properties may or may not > be relevant. > > You can certainly use g_rotacf if you think it will be meaningful; see > below regarding your .tpr file. > > <snip> > > tpbconv -s f.tpr -f f.trr -n f.ndx -o tpxout.tpr >> >> > > Don't use -f. If you do, tpbconv will think you are trying to create a new > .tpr file that starts off from the time frame present in the .trr file. Yes I removed -f and I got tpxout.tpr and used it for g_rotacf g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d but the result I got is like y=2x that starts at (0,0) which y=C(t) and x(Time,ps). Which is very strange... I don't understand what are these results using this command. (I should mention that f.xtc contains the coordinates of selected atoms). Many thanks for your attention and your help/Jamie > > > -Justin > > > -- > ======================================== > > 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 >
_______________________________________________ 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
