Hi,
I like the idea of having multiple time step in gromacs, but many
analysis tools would need a lot of rewriting, which would require more
work than changing mdrun. Or am I wrong?
Berk Hess skrev:
Hi,
Our philosophy up till now has been to remove the fastest motions
(using constraints and virtual sites) allowing for a larger time step,
instead of using a multiple time step algorithm.
Having a multiple time step algorithm would be nice, but this
would cause a lot more communication in the parallelization.
It would also make the code more complicated than it already is.
Berk.
------------------------------------------------------------------------
> From: [EMAIL PROTECTED]
> Date: Tue, 13 May 2008 12:16:04 +0200
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] multiple time step algorithm
>
> Dear David av der Spoel
>
> Thanks for answering. I was just curious to know why you chose not
to implement them.
> Have a nice day
>
>
> On Tue, 13 May 2008 12:00:43 +0200, David van der Spoel said:
> >
> > Cristina GRECO wrote:
> > > Dear Gromacs users and developers,
> > >
> > > it seems to me that Gromacs does not allow for multiple time
step nor
> > adaptive timestep MD. Is that correct or did I miss something? If
that's
> > true what's the reason ? For example, would there be problems in
running
> > such algorithm in parallels?
> > >
> > > Thanks to all
> >
> > Because no one implemented it.
> >
> > >
> > > Cristina Greco
> > >
> > >
> > >
------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D.
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
> > _______________________________________________
> > gmx-users
> > mailing list gmx-users@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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
------------------------------------------------------------------------
Express yourself instantly with MSN Messenger! MSN Messenger
<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
