[gmx-users] new default value for emtol with gromacs 3.3???
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 15 14:06:29 CEST 2007
Jennifer Rendell wrote:
> Dear gromacs developers and users,
> I sent a message several weeks ago and have had no response. I am unsure
> if this means it is a silly question or that no-one had an answer or
> just that no-one got around to replying. It is with great trepidation I
> send this again! ;-)
> 1. I notice that the default value for emtol has changed from 100.0
> kJ/mol/nm gromacs 3.2 and earlier, to 10.0 kJ/mol/nm (gromacs 3.3). Can
> someone explain why? I did search through the web site, but found
> nothing. In particular, I looked at:
> Revision History: nothing listed for emtol.
> Updates: including "Changes from 3.2 to 3.3 (under construction)" page,
> no reference to emtol.
> 2. I understood the energy minimisation was 'good enough' when it ran
> successfully down to emtol = 100. Is it now recommended that we go down
> to emtol = 10?
I am not sure when the new minimizer (l-bfgs) was introduced, that is
more powerful, and more prone to go that low. Anyway it depends on your
application. For normal mode analysis you need a lot better than 10, but
otherwise it is not a big deal whether it is 10 or 100.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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