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

From: Fangqiang Zhu (
Date: Tue Dec 02 2003 - 00:38:01 CST


Regarding your Q1, first of all, how do you define the "global rotational

As far as I know, the way NAMD removes COM is to simply offset every
atom's velocity by -COM. By doing this the resulting COM will be 0.


Shantenu Jha wrote:

> 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'?
> Thanks.
> Shantenu
> ===
> 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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