[gmx-users] overcome the integration problem (installing CVS)

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 11 17:21:17 CEST 2007

Michael Shirts wrote:
> 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?
> 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.
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 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://folding.bmc.uu.se

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