Re: Extraction of force data

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Mar 23 2007 - 23:36:03 CDT

The center of mass of what? The COM of the smd atoms is included in
the log file on every SMD line; I think it goes something like "SMD
timestep COM force" but you should check that against the manual.
Also the furthest distance of what from the COM?

On Mar 23, 2007, at 1:00 PM, Viral D. Tejani wrote:

> Hi,
>
> 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: http://www.ks.uiuc.edu/Training/Tutorials/
>> 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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