MD trajectory analysis

From: Deng, Jinxia (Nancy) (
Date: Thu Jan 28 2016 - 13:02:14 CST

Dear NAMD users,

Wonder what tool you use to analyze trajectory which is generated by NAMD.

Or if this topic has been well documented or discussed, wonder how to access the archive…

Any input is highly appreciated.


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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