On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Moeed wrote: > >> 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. >> >> > For all but the simplest systems this simulation length and data analysis > period is insufficient. How big is your polymer? Proper sampling may take > tens to hundreds of ns of data collection. > > Thanks. There are about 250 backbone carbons on 4 chains. Molecular weight of each chains is around 3700 g/mol. I have been looking at total energies and densities to equilibrate by checking sign change of Tot-Drift for these properties before 5 ns. I actually dont see a big change in energies. Is there any criteria to check on this using RMSD or error? (so far I have been using sing change of Tot-Drift). Please guide me. Thank you. > -Justin > > Best, >> moeed >> >> >> On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> 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 <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<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<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<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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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