[gmx-users] new default value for emtol with gromacs 3.3???

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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