Re: minimization

From: Nd S (navdeep79_at_gmail.com)
Date: Fri Sep 26 2008 - 10:12:00 CDT

Hi Chris

Can you please explain *minLineGoal*.

Also In minimization we define only the number of steps, is there any
criteria to terminate minimization before the number of mentioned steps.

Thanks
Navdeep

On Fri, Sep 26, 2008 at 7:19 AM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node11.html#996
>
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node29.html#8242
>
>
> On Fri, Sep 26, 2008 at 7:03 AM, jose correa <corrjose_at_gmail.com> wrote:
> > 2008/9/25 Audrey Salazar <alsalazar_at_u.northwestern.edu>:
> >> Hi
> >> So there is a bit more to this explanation, but it isn't phrased the
> best
> >> way, so I am going to just send this to you. I think that the point of
> >> "minimize" is to get rid of high-energy spikes caused by how
> "artificial"
> >> the initial configurations of the system usually are. If you would like
> >> more information, I can send you URL's for other relevant posts on the
> >> listserv tomorrow that might help explain what is going on in different
> >> words.
> >>
> >> Thanks,
> >>
> >> Audrey
> >>
> >> On 9/25/08, jose correa <corrjose_at_gmail.com> wrote:
> >>>
> >>> Dear all
> >>> I see that somebody carry out the protein minimization at 0, 300, 310
> >>> K or other gays mention that this step is temperature-independent of
> >>> the protein-membrane-water, according your experience, what is the
> >>> most recomendable?.
> >>> Best wishes
> >>>
> >>> Jose Correa
> >
> >
> > Dear all, thank you for help me. Andrey, if you have more information,
> > please send me that.
> > Best wishes
> > Jose
> >>
> >>
> >
> >
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar> Fax:
> 217-244-6078
>
>

-- 
--------------------------------------------
Gig'em
Navdeep Singh

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