Re: Extraction of force data

From: Viral D. Tejani (
Date: Fri Mar 23 2007 - 13:00:51 CDT


Thanks for the help Marcos and JC. It turns out that I was using an old
NAMD tutorial. The script on the new tutorial on the UIUC website
worked without problems.

My second problem is that, while I can get my force vs time data, I am
also attempting to get the displacement data, based on the coordinates
of center of mass and the furthest distance from the center of mass at
each time step. I am unsure how to extract these center of mass
coordinates from my simulation output files. However, once I can obtain
the coordinates, I can attempt to calculate the displacements based on
the data.

How can I extract the center of mass coordinates from my output files?
Any assistance is appreciated.

- Viral

Marcos Sotomayor wrote:
> Hi Viral,
> Those commands should be typed in a unix terminal, not the TkConsole
> (in case you are using a unix machine). If you are using Windows, you
> may want to check the latest Windows version of the tutorial available
> at:
> which I believe contains a different script to perform the same task.
> Marcos
> On Thu, 22 Mar 2007, Viral D. Tejani wrote:
>> Hi,
>> I am not too experienced w/ NAMD, and am practicing force extraction
>> using the NAMD Tutorial. From the TkConsole, I used the following
>> command and am getting the following results. (I copied and pasted
>> the exact text from the TkConsole)
>>> Main< (Tutorial) 4 % dir
>> .:
>> ubq.pdb ubq.psf ubq_wb.pdb ubq_wb.psf ubq_ws.pdb
>> ubq_ws.psf ubq_ww_eq.pdb ubq_ww_eq.ref ubq_ww_eq2.ref ubq_ww_pcv.dcd
>> ubq_ww_pcv.log
>>> Main< (Tutorial) 5 % cat ubq_ww_pcv.log | awk {if ($1=="SMD") print
>>> $0}'>
>> analysis/smd.dat
>> can't read "1": no such variable
>>> Main< (Tutorial) 6 %
>> I am using the same output files as provided by the NAMD website, and
>> do not know why this error is being generated and how to correct it.
>> Any assistance is appreciated.
>> - Viral

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