[gmx-users] how long simulation takes to get stable when constrains is none in mdp file?

[wang kelvin]

Thanks for reply

RMSD means root mean square deviation.
I am researching DMSO properties during phase changes from nomal temperature
to low tempreture.
At first step,I want to produce fully equilibrant systems at different
temperature. Of course ,there are many important parameters computed ,which
can be used to judge whether stable state reaches .
But RMSD's curve is relatively smooth , and covenient to see .So I take it
as most important parameter to judge equilibrium. Only when RMSD plot
level, i do other computation and see whether they reach equilibrium too.


Your sincerly



wang


2008/8/5, Tsjerk Wassenaar <tsjerkw at gmail.com>:
>
> why RMSD?
>
> On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
> > wang kelvin wrote:
> >>
> >> hi:
> >>  i am doing simulation of  a system consists of  512 DMSO moleculers and
> >> 917 water moleculers.
> >> the whole system is running under 290K and 1bar ,and constraints = none;
> >> the simulation has taken 8000 ps ,but it seems not to get stable
> >> yet,because RMSD keeps rising.
> >> when i did simulation of the same system with constraints set
> all-bonds,it
> >> usually get stable within 3000ps.
> >> i wonder whether any mistakes has been made or it is normal.
> >> can you give some hints?
> >> thanks.
> >
> > what rmsd?
> >
> >>
> >>
> >> ------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > _______________________________________________
> > gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080805/e6ba1ab6/attachment.html>