RE: energy output

From: Deng, Jinxia (Nancy) (
Date: Wed Dec 09 2015 - 13:12:11 CST

Thank you All for your response. I will start from there ☺


From: Jeffrey Potoff []
Sent: Wednesday, December 09, 2015 12:57 PM
To:; Deng, Jinxia (Nancy)
Subject: Re: namd-l: energy output

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 Deng, Ph.D. | Principal Scientist, Computational Chemistry & Molecular Modeling
Zoetis Inc| Global Therapeutics Research | 333 Portage Street, Kalamazoo, MI 49007
Office: 2693599121 |<>

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;
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

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