Re: Forces on Atoms and Potential Energy

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Feb 17 2009 - 14:29:52 CST

Just from glancing at the script, my suggestion would be to move the
file open command before the calcforces procedure and then pass the
handle to the procedure using "global $fileID_check". See the User-
defined Forces tutorial also for more ideas: http://www.ks.uiuc.edu/
Training/Tutorials/

On Feb 16, 2009, at 1:57 PM, Mohamed Seyam wrote:

> Hello,
>
> I am trying to run an namd simulation on a double stranded DNA. I
> want to find the total forces on each atom and the potential energy of
> each atom throughout the simulation. I tried using the script on the
> thread:
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7140.html
>
> When I put this script in the config file, it gives me an error:
>
> FATAL ERROR: couldn't open "forces.txt": too many open files
> while executing
> "open $filename_check "a""
> (procedure "calcforces" line 4)
> invoked from within
> "calcforces"
>
> My simulation contains 8229 atoms. Also, is there any way to find the
> potential energy of every atoms? I looked through the thread, but
> couldn't find an answer.
>
> Thanks,
>
> -Mohamed Seyam

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