rotational energy, Tcl and environment variable(s) in Linux 2.5

From: Shantenu Jha (
Date: Sun Nov 30 2003 - 18:47:07 CST

Dear NAMD Junkies,

I'm try to script a set of simulations so as to be able to remove the
centre of mass and global rotational energy, say every 10E5 timesteps.

The approach I'm taking is to a start a simulation, run for the 10E5
steps, checkpoint (coor, vel and xsc) and then restart as a new
simulation. I'm using the default value of COMmotion which takes care of
the centre of mass motion at the beginning of each (sub)simulation.

Q0: Is there a more elegant &/or efficient way to do this?

Q1: How to remove global rotational energy?

Q2: When I try to set a variable in my NAMD config file by reading in an
environment variable, the environment variable is not being parsed (at
all). This problem is unique to the Linux precompiled binary (2.5), as all
works well using the precompiled Origin (MPI) binary. (The environment
variable is being set by a driver perl script, but I've set it by hand and
checked for correctness using 'echo $...')

I've attached below the relevant part of the config file. Any ideas?

Since I'm at it can I also ask, how NAMD goes about adjusting initial
velocities to remove COM motion of the sytem on using 'COMmotion no'?



set run_num $env(RUN_NUM)
set first_timestep $env(FIRST_TIMESTEP)
set run_step $env(RUN)

restartfreq $run_step

outputname evris24.$run_num
extendedSystem evris24.0.$first_timestep.xsc
bincoordinates evris24.0.$first_timestep.coor
binvelocities evris24.0.$first_timestep.vel

firsttimestep $first_timestep
run $run_step

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