help: how to scale the velocities by a factor for a subset of the system?

From: Yong Zhang (
Date: Tue Sep 05 2006 - 21:59:25 CDT


I want to run a trajectory, which will restart from a equilibrated structure
(from a previous run with coordinates and velocities saved). In the
beginning of this trajectory, I need to modify the velocities of some atoms
in the system by multiplying a factor to the equilibrated velocities. In
CHARMM, this can be done by using "scalar", "multiple <factor>" and
"select". I can do this using charmm by: read velocities --> modify the vel
using above commands --> output in pdb format--> read into NAMD and run the
traj. But as indicated by the manual, the non-binary pdb file has lower
accuracy than the binary ones. So I am wondering if there is a simple way
within NAMD to do this? Or is there a way to solve this problem, like using
simple code?
I am a beginning of NAMD. I read through the manual but did not find
answer. I appreciate your help.

Best wishes,

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