[gmx-users] T-coupling of water and ion
feenstra at few.vu.nl
Thu Jun 2 11:38:22 CEST 2005
Jian Zou wrote:
> # time T_SOL T_SOL x 1.5
> 0 263.260 394.89
> 20 267.164 400.746
> It seems to be the ref_t I defined for "SOL" tc_group in my mdp.
> In the same way, should I get the factor for the "RNA" tc_group, and get
> the "400K" as the ref_t.
> Is this correct?
Yes. Count the number of bonds in your RNA (usually the same as the
number of atoms-1), these will be constrained.
> But how about the temperature for sodium cation in my system?
> How to explain the large fluctuation in both g_traj result and g_energy
> Do these results imply large heat transfer from Na+ and SOL?
No, you only have a few ions, so the fluctuations are large compared to
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