Re: help!!

From: JC Gumbart (
Date: Thu Jun 14 2007 - 14:07:59 CDT

Force data cannot be extracted from the dcd file. The script ft.tcl
reads data from the log file, so if you did not edit the script to
change the log file it reads, that could explain why you get the same
plot twice.

  I found the script here:
namd/namd-tutorial-files/3-1-pullcv/ but in the future, please cut
and paste any scripts you are using into the email.

On Jun 14, 2007, at 6:43 AM, shivam ghosh wrote:

> Dear namd users,
> I am using steered molecular dynamics with constant velocity to
> simulate the unfolding of a rna molecule.
> For two different speeds(0.01,0.05 A/fs), keeping the DCD and
> SMDOutput frequency the same, the force acting on the SMD atom is
> different at same time( same frame number) as seen from the .log file.
> However the plot of force versus frame number is the same for both
> speeds when it is extracted from the dcd file using ft.tcl.
> I expect the slope of the two plots to be different, am i
> understanding something wrong or have i made a mistake in the input
> file?
> I will be grateful for any suggestions.
> Regards
> Shivam
> PS.I am interested to calculate work done on the system due to
> constant velocity pulling so i need the force acting on the centre
> of mass of the molecule due to the pull. Please give me suggestions
> how i can calculate this force.

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