Re: Accessing atoms and velocities during NVE run

From: Axel Kohlmeyer (
Date: Fri Feb 06 2009 - 15:42:20 CST

On Fri, 6 Feb 2009, Nd S wrote:

NS> Hey Cris
NS> First of all thanks a lot for the quick response.

NS> My problem is a carbon nanotube at the center of the cell surrounded by
NS> liquid molecules. What I want to do is a constant heat flux simulation, by
NS> constantly putting energy into the nanotube and removing the same amount
NS> from the outside periphery of the cell. So for constant heat flux into the
NS> nanotube, I am trying to get the velocities of the atoms of the nanotube and
NS> rescale them depending on the calculations. Also by the same way, I will
NS> rescale the velocities of the atoms on the periphery of the cell to remove
NS> heat.

have you considered using LAMMPS for that purpose?
it has very convenient tools to do this out-of the box.

for the typical bio-system (for which NAMD is somewhat
optimized for) LAMPS is 2-3x slower, but for the kind of
simulation that you want to do, it may actually run faster,
_and_ you don't have to make NAMD jump through hoops.

just a thought,


NS> Also doing this simulation, I am not sure if I can use periodic Boundary
NS> condition or not. Any help will be highly appreciated.
NS> Thanks
NS> Navdeep

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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