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

[David van der Spoel]

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.
________________________________________________________________________
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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