From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
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
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.
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu 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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