[gmx-users] Minimisation engine

[David van der Spoel]

On Thu, 18 Dec 2003, Hua Wong wrote:

>> >Hello,
>> >I would like to know the differences between GROMACS CG engine and NAMD's ?
>> >Because NAMD can minimise far much better big proteins that would take a
>> >hell of a time to minimize with CG under GROMACS.
>> >
>> 
>> try the beta version, the minimizers are greatly improved. 
>> 
>> >Thanks
>> >
>> 
>> 
>
>I will give a try with the beta.
>
>But I still don't know the difference between the two minimisation engine. 
>They are both about conjugate gradient after all? Why does one software 
>minimise, while one can make a run 'till domesday.....
>
>I apologise in advance if it is a stupid question, but I am a real dork in 
>math and physic...
>

It's not entirely trivial, but there are a number of parameters involved 
(not many though) that influence the behaviour. Some of these 
are probably built-in (i.e. hardcoded). Furthermore the steepest 
descents in gromacs3.1.4 is not very good. 

>Thanks
>
>

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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