From: Gianluca Interlandi (gianluca_at_bioc.unizh.ch)
Date: Thu Apr 22 2004 - 05:56:39 CDT
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
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