# Re: minimum energy frame

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Wed Apr 26 2006 - 09:26:53 CDT

Hi all,

I've found a reference (http://www.ks.uiuc.edu/Research/vmd/plugins/namdplot/) to a plug-in called NAMD Plot, but I can't find the plug-in itself. This might do what I'm looking for Does anybody have any tips as to how I might obtain it and get it to work?

Richard

Richard L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030
rwoodphd_at_yahoo.com

----- Original Message ----
From: Richard Wood <rwoodphd_at_yahoo.com>
To: namd-l_at_ks.uiuc.edu
Sent: Tuesday, April 25, 2006 11:45:33 AM
Subject: namd-l: minimum energy frame

<!-- DIV {margin:0px} -->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
rwoodphd_at_yahoo.com

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