[gmx-users] Re: velocities not rescaled

[Viswanadham Sridhara]

Hi David,
Its from one of the journal papers. Let me post what it said.
----- This is what the paper says-----
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.    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.

--------
Thanks David.
On 1/19/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Viswanadham Sridhara wrote:
> > Hi everyone,
> >
> > I am reposting my earlier question, as I thought you might have missed
> it.
> >
> > I am not quite able to understand the meaning of " The velocities of the
> > atoms were not scaled during the simulation". Then how can we use the
> > temperature coupling?
>
> Where does this message come from?
>
> We need more info if you want answers to such questions. I have never
> seen this message before.
>
>
> > Thanks,
> > Vissu
> >
> > On 1/18/06, *Viswanadham Sridhara* <muta.mestri at gmail.com
> > <mailto:muta.mestri at gmail.com>> wrote:
> >
> >
> >     Hi everyone,
> >     I am not quite able to understand the meaning of " The velocities of
> >     the atoms were not scaled during the simulation". Then how can we
> >     use the temperature coupling?
> >     Thanks,
> >     Vissu
> >     --
> >     Viswanadham Sridhara,
> >     Graduate Research Assistant,
> >     Old Dominion University, "VIRGINIA".
> >
> >
> >
> >
> > --
> > Viswanadham Sridhara,
> > Graduate Research Assistant,
> > Old Dominion University, "VIRGINIA".
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> 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://xray.bmc.uu.se/~spoel
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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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