[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  
Temperature                   303.3    474.854    474.854 -3.75465e-05 

probably because thie .edr was generated by eneconv on all my 200 ps 
Indeed, g_energy on a single segment gives me a sensible RMSD value.

Thanks again,

-- 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 
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):


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