Re: any SD minimization in NAMD?

From: L. Michel Espinoza-Fonseca (
Date: Fri Jul 14 2006 - 11:36:09 CDT

Hello Jasmine,

If you want to use a simple program to do minimization by using either
SD or CG, you could use the freely available Swiss PDB viewer. It uses
the GROMOS ff and can be little bit slow, but it might be useful for
your purposes.


2006/7/13, Ching Wong <>:
> Hi,all NAMD users.
> Is CG (conjugated gradient) the only way of minimization provided by
> NAMD? I am wondering if it's fairly okay to do without SD (steepest
> descent). Some books mention about minimization protocol of using SD
> then CG (or other combinations). Do you always include SD in your
> protocol and do it with some other programs? Any suggestion of
> programs? Or do you think it is not necessary to use SD for crystal
> structure or homology model?
> Thanks in advance. And thanks for everybody that answered my past
> questions. :)
> Sincerely,
> Jas
> -------
> Jasmine

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