[gmx-users] T-coupling of water and ion

[Anton Feenstra]

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.

Right.

> 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 
> result?
> 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 
the average.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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