[gmx-users] "Angular" Vs. "Linear" in NVE simulation
baptista at itqb.unl.pt
Mon Nov 7 17:47:15 CET 2005
On Fri, 4 Nov 2005, David wrote:
> On Fri, 2005-11-04 at 23:32 +0800, Xiaobing Feng wrote:
>> Dear everyone,
>> When I run a NVE simulation with "Angular" the
>> total energy decreased very rapidly, though the
>> system is equilibrated with NPT. Once "Angular" was
>> replaced by "Linear" the total energy is well
>> "Angular" removes the drifts of both center-of-mass
>> and angular, so, it seems better to use "Angular".
>> Could anybody give me an explanation why "Angular"
>> is bad in NVE?
> Not sure. It could be a precision problem, but I think we have tried it
> in double as well. Have you tried that?
If you are using periodic boundary conditions (pbc) in your NVE
simulation, angular momentum _should_ not be conserved, regardless of the
precison you use. Conserved quantities are a consequence of symmetry
properties: linear momentum is conserved when space is homogeneous
(invariant under translation); angular momentum is conserved when space is
isotropic (invariant under rotation). Now, the use of pbc does not mess
you the homogenity of space, but kills its isotropy because it does not
have spherical symmetry. When you don't use pbc (eg, when simulating a
cluster) the space is sperically symmetric and angular momentum _should_
This issue is mentioned in most simulation textbooks (Allen & Tildesley,
Leach, etc). If you are curious about these symmetry matters you can have
a look at the Feynman Lectures for a nice overview, or even at Goldstein
(classical) or Messiah (quantum) for the heavy stuff.
>> Many thanks in advance
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica, EAN, ITQB II, Apartado 127
2781-901 Oeiras, Portugal
phone: +351-214469619 email: baptista at itqb.unl.pt
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