[gmx-users] heat exchanges
Chris Neale
chris.neale at utoronto.ca
Thu Feb 5 21:08:26 CET 2009
Thank you Berk,
I have checked my temperature and find that there is no difference while
using tau_t=0.1 or 1.0 (~2 ns):
tau_t=0.1: temp=303.36 +/- 1.90
tau_t=1.0: temp=303.31 +/- 1.98
While using only one temperature coupling group, how would I ensure that
the temperature of water is
the same as that of DPC?
I do see the large depression of diffusion that is induced by tau_t=0.1
and is pointed out in your thesis:
Diffusion of tip4p:
tau_t=0.1: 1.43 +/- 0.003
tau_t=1.0: 2.81 +/- 0.136
md with berendsen = 3.115 +/- 0.056
Diffusion of DPC detergent:
tau_t=0.1: 0.0323 +/- 0.003
tau_t=1.0: 0.137 +/- 0.02
md with berendsen = 0.0928 +/- 0.045
PS: Note that the RMSD values for the temperature above are from my own
calculation as those from g_energy
in gmx 3.3.1 and 4.0.3 are nonsensical to me :
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 303.3 474.854 474.854 -3.75465e-05
-0.0976211
probably because thie .edr was generated by eneconv on all my 200 ps
segments.
Indeed, g_energy on a single segment gives me a sensible RMSD value.
Thanks again,
Chris.
#####################
-- original message --
Yes, the SD "thermostat" has the huge advantage that it thermalizes each
degree of freedom separately.Therefore you never have incorrect temperature
distributions in your system, unless you have very serious integration
artifacts. SD also avoid any ergodicity problems.
BTW You should check your temperature for your SD runs with tau_t=1.
I often use 1, but that is with a shifted LJ potential and not with a
twin-range
setup that introduces some errors. You might need to change to tau_t=0.5.
tau_t=1 has nearly no effect on the dynamics of water, whereas tau_t=0.5
slows it down somewhat. See chapter 2 of my thesis for numbers for SPC
(which diffuses twice as fast as real water):
http://dissertations.ub.rug.nl/faculties/science/2002/b.hess/
Berk
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