Hi,
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.
Cheers,
Erik
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.
______________________________________________________________________
__
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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