[gmx-users] Minimisation engine

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 18 21:27:00 CET 2003

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. 


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

More information about the gromacs.org_gmx-users mailing list