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

From: Shantenu Jha (s.jha_at_ucl.ac.uk)
Date: Thu Dec 04 2003 - 15:59:10 CST

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

.. as rotational kinetic energy.

FWIW, I'm concerned with the type of problem as mentioned in:

@Article{ ,
  author = {Stephen C. Harvey and Robert K.-Z. Tan and Thomas E.
Cheatham},
  title = {The Flying Ice Cube: Velocity Rescaling in Molecular
                  Dynamics Leads to Violation of Energy Equipartition},
  journal = {Journal of Computational Chemistry},
  year = {1998},
  volume = {19},
  number = {7},
  pages = {726},
}

Shantenu

> 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
>
>

-- 
--Shantenu Jha,  Research Fellow
Centre for Computational Science
University College London  (UCL)	http://www.realitygrid.org
s.jha_at_ucl.ac.uk    020-7679-5300        PGP Key ID 0x78F823E6

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