Re: minimum energy frame

From: LEWYN LI (
Date: Tue Apr 25 2006 - 12:39:23 CDT

Dear Richard,

         Are you familiar with the LINUX environment and script languages
such as awk? If yes, here is my "quick-and-dirty" solution. Using LINUX,
you can first extract all the energy lines:

grep ENERGY output.log > output2.dat

         You can then use awk to extract the columns you want (x = step,
y = total energy):

awk {'print $x " " $y'} output2.dat > output3.dat

         You can then quickly plot output3.dat i.e. plot energy as a
function of step. Visually identify the minimum, and find the
corresponding frame in your trajectory. Or you can write a short program
in C or any other language convenient for you to extract the minimal

         Hope this helps!


On Tue, 25 Apr 2006, Richard Wood wrote:

> Hi all,
> I've currently involved myself in a rather time consuming project. I'm
> running 1 ns of dynamics and I'd like to be able to find the minimum
> energy frame from these 10000 steps that are saved in my trajectory
> (1000000 steps in the output file), and write out the value of this
> minimum energy and save the correspondin coordinates to a .pdb (or
> .coor)
> file. What I am currently doing is opening the output file in MS Word,
> cutting it into pieces, opening the pieces in MS Excel, finding the
> minimum energy for each piece, recording these, the finding the overall
> minimum, and going back and locating the step number that corresponds to
> this minimum energy. Then I save the coordinates that frame from my
> trajectory using NAMD. These coordinates then go into the next MD
> calculation.
> This whole process takes about 2 hours or so, almost the entire time it
> takes for my MD calculation to run. Surely there must be a better way
> to do this, using NAMD or a NAMD-like script.
> I'd appreciate any suggestions on how I can do this more effeciently,
> as I have 42 such calculations to analyze and run. As it stands now,
> with other things I have to do, it takes about a day to do one of these.
> So I'm looking at this bein a 6 week process, unles I can somehow speed
> the analysis part up.
> TIA,
> Richard
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030

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