[gmx-users] Re: velocities not rescaled

[X.Periole]

> Alamethicin Helices in a Bilayer and in Solution: 
>Molecular
> Dynamics Simulations
> D. Peter Tieleman,* Mark S. P. Sansom,# and Herman J. C. 
>Berendsen*
> ...................
> The pros and cons of this approach have
> been
> discussed by, e.g., Tobias et al. (1997). Water, lipid, 
>and protein were
> coupled separately to a temperature bath at 300 K, with 
>a coupling constant
> tT 5 0.1 ps.      The velocities of the atoms were not 
>scaled during the
> simulation.    
Probably refering to NVE simlations where you check the
temperature at regular time intervals and rescale the
velocities to correct of a drift of the temperature. That
is (was) very common use in CHARMM procedures, in NVE.

> Although the use of separate temperature 
>baths for different
> components of the system may be considered unphysical, 
>it is necessary to
> avoid temperature gradients, and the parameters used 
>have been chosen
> empirically to minimize the known drawbacks of this 
>procedure.
> 

At that time there were discussion about the physical
meaning of using different T bath for prottein, solvent 
and
lipid.

The rest of hte paper probably gives sense to this 
comments.

XAvier