SMD-velocity unit

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Sat Jan 10 2004 - 18:24:18 CST

Hi namd users,

I am not sure about the following.
Say I use a value of 0.001 for the SMD velocity. The manual says that the
unit corresponding to this velocity is Angstroms/timestep.
The timestep in the MD simulations is 1fs however I print the output in
the SMD every 100 steps. So is the velocity
1. Angstroms/fs
2. Angstroms/(fs*100)

I would say that the first answer is the correct one.
Assuming that the velocity is expressed in Angstroms/timestep of MD
integration, I want then
to calculate the work using the formula in the tutorial on the NAMD web
site
W=v*dt*cumsum(f)
I use here v=0.1A/ps, dt=0.1 ps (I print the output every 100 steps).
However in the SMD I also have the r_CM of the SMD atoms output at every
step, thus I could also calculate
W=sum[del_r_cm*f]
The two values are however different (there is one order of magnitude
difference between the two values).

Any comment?

Thanks,
Ioana

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