Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500 ps NVT was done as equilibration) and total energy has been equilibrated after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf. Best, moeed On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul <[email protected]> wrote: > > > Moeed wrote: > >> Dear users, >> >> I have created radial distribution function plot for Carbon atoms in a >> system containing polymer chains. I see some little jumps between first and >> second peak. >> I need your help to comment on how this behavior can be justified (or if >> the plot is wrong). >> >> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx >> > > How long is the sampling? In the absence of -e and with -b being hidden > from us for some unknown reason, it's hard to guess. I'd say your > simulation just isn't fully converged, although for complex systems that can > be a challenge anyway. Nothing unusual. > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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