From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Wed Dec 09 2015 - 11:56:45 CST
On 12/9/2015 12:39 PM, Deng, Jinxia (Nancy) wrote:
>
> Dear users,
>
> I am fairly new to use NAMD, and wonder how to get energy profile in a
> separate output file during time course. Currently, it seems
> everything just print out on the screen or in a directed output file
> which has many other information as well…
>
> Thanks and looking forward to hearing from you.
>
> Nancy
>
> *Nancy Deng, Ph.D. *| Principal Scientist, Computational Chemistry &
> Molecular Modeling**
>
> Zoetis Inc| Global Therapeutics Research | 333 Portage Street,
> Kalamazoo, MI 49007
>
> Office:*2693599121 | jinxianancy.deng_at_zoetis.com*
>
Hi Nancy,
You can extract the energies using NAMDplot in VMD, or you can get
them out of the log file with an awk script, such as this. The
$<number> corresponds to a particular column in the energy table. So
you can get whatever energies you want by changing, or adding, the
variables in the list.
#!/usr/bin/awk -f
BEGIN{eave_total=0; count=0;nmolecule=500; nequil=200000}
{if($1 = /ENERGY:/ && $2>nequil)
{ print $2, $14;
eave_total += $14;
++count;
}
}
END{print "Potential energy average
=",eave_total/nmolecule/count,"kcal/mol\n"}
-- Jeffrey Potoff Professor & Director of Early Engineering Programs Department of Chemical Engineering and Materials Science Wayne State University http://potoff1.eng.wayne.edu http://gomc.eng.wayne.edu
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