[gmx-users] new default value for emtol with gromacs 3.3???
lindahl at cbr.su.se
Tue May 15 14:20:08 CEST 2007
The default value is just set reasonably high so we avoid lots of
mailing list questions about the message that "energy minimization
finished without converging to the requested precision".
For MD it doesn't matter much at all, and for NMA you should set it
to 0 and run double precision minimization until convergence.
On May 15, 2007, at 2:06 PM, David van der Spoel wrote:
> 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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