[gmx-users] Temperature of the system when using stochastic dynamics in vacuum

[钩深致远]

Hi all,

Recently, I run a carbon nanotube in vacuum using stochastic dynamics
(Gromacs 3.3.1, integrator=sd) at 300K (ref_t=300.0) for 800 ps. The number
of atoms of the CNT is about 5000, and the tube is left free to vibrate
except for a few atoms are position restrained. When I set the tau_t=100,
0.2, 0.05, the actual simulation temperature fluctuates around an average
value ~72K, 283K, 299K respectively.

I also run a peptide with about 110 atoms in vacuum using stochastic
dynamics at 300K for 1 nanosecond. When I set the tau_t=100, 0.1, the actual
simulation temperature fluctuates around an average value ~147K, 302K
respectively.

So I want to know: Why different tau_t (with the same ref_t=300.0) can
result in different temperature when the system is in vacuum? Can I perform
the stochastic dynamic simulation in vacuum? If I can, can I used the tau_t=
0.05, 0.1 for the CNT and peptide mentioned above respectively to couple the
temperature of the system to 300K?

 Thanks,

 Xiu Peng.
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