From: Gianluca Interlandi (gianluca_at_bioc.unizh.ch)
Date: Fri Apr 23 2004 - 03:59:45 CDT
Hello Brian,
Many thanks for your explanations. This means that the time it takes
untill the temperature drifts to the desired temperature (10ns) can be
regarded as "equilibration".
But, how do you fix then the temperature in the NVE ensemble? Is it simply
assigned at the beginning with "temperature" and nothing else?
Thanks,
Gianluca
On Thu, 22 Apr 2004, Brian Bennion wrote:
> Hello Gianluca,
>
> if no coupling is asked for none is received. Without any temp bath you
> are riding the effeciency of the integration scheme in NAMD (verlet).
>
> I routinely run without any coupling, ie NVE ensemble, if your system is
> properly equilibrated then temp baths can be discarded within this
> ensemble.
>
> My training taught me that coupling, especially temperature
> coupling was "bad", in that you technically start a new simulation
> everytime you bleed energy off the system.
>
> So thats my $0.02
>
> Brian
>
>
> On Thu, 22 Apr 2004, Gianluca Interlandi wrote:
>
> > Hi all,
> >
> > I have to re-post this message in a more detailed fashion, as it is really
> > worrying me.
> >
> > I have done many simulations with NAMD, where I have coupled the system to
> > a Nosé-Hoover Langevin piston pressure control with the following
> > parameters:
> >
> > langevinPiston on
> > langevinPistonTarget 1.01325
> > langevinPistonPeriod 100.
> > langevinPistonDecay 50.
> > langevinPistonTemp 400
> >
> > I also wanted to couple the system to a heat bath to keep the temperature
> > constant:
> >
> > tCouple on
> > tCoupleTemp 400K
> > tCoupleCol B
> >
> > I have realized later that the values in the B-column of the
> > coordinate-file were all set to zero. This means, that I didn't have any
> > temperature coupling. When I plotted the temperature in function of the
> > frames, I saw a drift from 350K to 407K during 10ns. What has happened?
> > What did bring the temperature to the desired value? Is there any hidden
> > temperature coupling or temperature scaling, when none is specified?
> >
> > I would be very glad to get a hand from anyone out there.
> >
> > Many thanks,
> >
> > Gianluca
> >
> > -----------------------------------------------------
> > Gianluca Interlandi gianluca_at_bioc.unizh.ch
> > +41 (0) 1 635 55 93
> > +41 (0)79 655 73 35
> > http://biocroma.unizh.ch/gianluca/
> >
> > PhD-Student of the Department of Biochemistry
> > at the University of Zurich Irchel, Switzerland
> > -----------------------------------------------------
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>
>
-----------------------------------------------------
Gianluca Interlandi gianluca_at_bioc.unizh.ch
+41 (0) 1 635 55 93
+41 (0)79 655 73 35
http://biocroma.unizh.ch/gianluca/
PhD-Student of the Department of Biochemistry
at the University of Zurich Irchel, Switzerland
-----------------------------------------------------
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