Re: minimization

From: Audrey Salazar (alsalazar_at_u.northwestern.edu)
Date: Fri Sep 26 2008 - 11:41:13 CDT

Hello
Some other posts regarding the goals of minimization:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5403.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5405.html

I hope they are useful.

Audrey

On 9/26/08, jose correa <corrjose_at_gmail.com> wrote:
>
> 2008/9/25 Audrey Salazar <alAs per this information that I found on the
> listserv:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5403.html
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5405.html
> salazar_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
> >
> >
>

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering
Northwestern University
Evanston, IL USA
Phone: 847.491.2188

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