Re: CCL:Velocity re-assignment

On Sat, 17 Nov 2001, Rick Venable wrote:
 >
 >However, one does not typically use values close to zero or infinity, so
 >in general, the ensemble isn't known.  By taking care with the piston
 >parameters, the extended systems also have minimal effect on the
 >dynamics of the system.  The early work by people such as HC Andersen
 >and WG Hoover, and later studies by ML Klein and others have shown this.
 I was basically recalling what is in my understanding in this paper:
 > at.at Article{Morishita2000a,
 >  author =      {T. Morishita},
 >  title =       {Fluctuation formulas in molecular-dynamics simulations
 >with the weak coupling heat bath},
 >  journal =     {J. Chem. Phys.},
 >  year =        2000,
 >  volume =      113,
 >  pages =       {2976-2982}
 >}
 I am not claiming that the older papers by Klein, Hoover etc. are wrong,
 but if you use a piston to keep the temperature this becomes part of the
 system, and hence you are not simulating the system you think you do. As
 far as I know most coupling methods influence the temperature
 fluctuations (necessary for computing heat capacities etc.), which can
 be quite easily seen by taking the fourier transform of the temperature
 fluctuations. These usually have a peak corresponding to the coupling
 constant of your piston.
 >The use of a piston for const T does correspond to the NVT ensemble; or
 >are you claiming that Allen, Tildesely, Andersen, Hoover, Klein, etc.
 >are wrong?
 See above.
 >I agree about equilibration (and said so in my orignal message), and
 >also about the use of Ewald methods, especially for true periodic
 >systems.  However, a protein in a cube (etc.) of water with periodic
 >images isn't really a true periodic system, because the effective
 >concentration is much higher than typical solution experimantal work.
 >In most cases, one doesn't want the field effect of the protein in the
 >adjoining image cell, and a cutoff may be needed to exclude it.
 One should always ask: "how do I minimise the artefacts on my system of
 interest." PME I think is less bad than cut-offs... One day when I am
 bored I will do the simulations with PME with ever increasing box size,
 and check the interaction between the protein and its image. See how far I
 have to go to simulate a protein at infinite dilution.
 On a side note, under physiological conditions (i.e. in a cell) the
 protein density is quite high. So why not simulate three or four proteins
 in a single simulation box with PME? The different proteins will average
 out any serious "crystal" artefacts due to PME and you can write four
 papers based on one extremely realistic simulation...
 Groeten, David.
 ________________________________________________________________________
 Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
 Husargatan 3, Box 576,  	75123 Uppsala, Sweden
 phone:	46 18 471 4205		fax: 46 18 511 755
 spoel at.at xray.bmc.uu.se	spoel at.at gromacs.org   http://zorn.bmc.uu.se/~spoel
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