From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Apr 26 2006 - 10:01:01 CDT
You can find it in the latest version of VMD. Go to
Extensions-->Analysis-->NAMD plot. Then load your output file and ask
NAMD to plot whatever you want to plot. If you want to save the data,
export it as "xmgrace" format. I read that you're using excel, so you
simply import the data from the file you created and analyze it.
Hope it helps,
Michel
2006/4/26, Richard Wood <rwoodphd_at_yahoo.com>:
>
> 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
>
> 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
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:58 CST