Re: How to write gradual heating config file

From: Audrey Salazar (alsalazar_at_u.northwestern.edu)
Date: Mon Aug 25 2008 - 18:23:41 CDT

Hello
Perhaps I should mention that I did try writing a for loop in Tcl that
would increase the temperature and "run" a certain number of time
steps in succession, but that was not well received by NAMD. I am at
a loss of what else to try. It looked something like this:

set temperature =300

for {set temp = 30} {$temp <= $temperature} {incr temp}{
run 300
}

Thank you again.

Audrey

On 8/25/08, Audrey Salazar <alsalazar_at_u.northwestern.edu> wrote:
> Dear NAMD-L,
> I am fairly new to NAMD and thus far, I have been able to navigate
> through NAMD and VMD using information from the tutorials. I would
> like to know if it is possible to make a script in the .conf file to
> perform gradual heating.
>
> After searching the NAMD-L archive for "gradual heating" I came upon
> this thread:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6440.html
> where Victor Ovchinnikov says that he includes a snippet of his code,
> but the snippet is not available on the archive.
>
> I realize from reading the Config file tutorial page
> (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html)
> that after commands like "run" or "minimize" that only a subset of
> commands may be used, but I am not sure what kind of a resource I
> should look for to do this.
>
> Example scripts would be especially helpful.
>
> Thank you in advance.
>
> Audrey
>
>
>
>
> --
> Audrey L. Salazar
> Amaral Research Group
> Dept. of Chemical and Biological Engineering
> Northwestern University
> Evanston, IL USA
> Phone: 847.491.2188
>

-- 
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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