From: shivam ghosh (
Date: Thu Jun 14 2007 - 06:43:31 CDT

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.


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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