From: "Michael Shirts" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: [gmx-users] Re:overcome the integration problem (installing CVS)
Date: Wed, 11 Apr 2007 16:39:20 -0400
How about total energy? In tends to be constant in NVE simulations. I
don't know what the conserved property would be in an NVT simulation.
David.
For most algorithms that give correct ensembles, there are
pseudo-energy properties that are conserved. For NVE, it's obviously
the energy. For Nose-Hoover NPT, there's a term involving the "mass"
of the coupling to the heat reservoir that, when added to the scaled
energy term produces a quantity that will be conserved. For
Parrinello-Rahman dynamics, there's a similar term involving the
coupling to the pressure bath.
It would.
Although I would still argue that when using a thermostat there
is in most cases no "useful" quantity that would be affected
by the current, very small, velocity inaccuracies.
Berk
I think algorithmic self-consistency could generally be justified as
useful. If one is applying a certain algorithm, it's good to have a
measure of how well that algorithm is being implemented, so one can be
sure that any errors are negligible. I agree with Berk that such
inaccuracies are small. But it's good to have a measure of how small
they are built in, just to be sure! :)
Best,
Michael
I have now programmed in the conserved quantity (not committed yet).
SPC water gives the same energy conservation in NVT Nose-Hoover as
in NVE.
I did a run of 100 ps for 216 SPC with dt=0.002 ps and SETTLE at 300 K,
tau_t=2 ps:
NVE: drift per degree of freedom -0.026 kJ/mol /ns
NVT: drift per degree of freedom -0.024 kJ/mol /ns
The difference seems to be within the noise.
That is reassuring.
Micheal, thanks for the suggestion!
Berk.
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