SMD force

From: Ioana Cozmuta (
Date: Sat Jan 03 2004 - 22:01:45 CST


Happy New Year to everybody and lots of successful simulations with NAMD
in 2004!

I have a short question related to SMD output. The manual says that at
every SMD step the program writes out
1. the current timestep,
2. the current position of the center of mass of the restrained atoms and
3. the current force applied to the center of mass (pN).

It is not clear to me what exactly does "current force applied to the
center of mass" means:
a. force due to dragging of the atoms with velocity v via a harmonical
constraint k
b. force due to the interaction with the surroundings
c. both dragging force and interaction with the surroundings

I want to use the information in the output to calculate only the
component due to the interaction between the restrained atoms and the

Thanks in advance for your answer,

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