From: "Michael Shirts" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
Subject: Re: [gmx-users] overcome the integration problem (installing CVS)
Date: Wed, 11 Apr 2007 11:15:08 -0400
Hi, all-
I would like to add that for a constant temperature ensemble the effect
of this fix is neglegible.
It is only useful for constant NVE simulations.
Berk.
I think this might need some qualifications. If the constant
temperature dynamics are based inherently on NVE dynamics, they must
be affected similarly. For example, for Nose-Hoover thermostats,
there exists a conserved quantity. I would expect that this fix would
also improve that conserved quantity, wouldn't it?
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.
One feature that would be useful is that for any algorithm that has a
"conserved energy-like" quantity, there should be an entry in the .edr
file with that quantity. It would be a useful check for algorithmic
consistency. I don't think this is yet in GROMACS, though I could be
wrong -- I haven't examined the CVS that recently.
It is not (yet) in Gromacs, but it would indeed be useful to have it.
Berk.
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