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

[Anton Feenstra]

zouj01 at mails.tsinghua.edu.cn wrote:
> tc-grps                  =  RNA SOL_Na
> tau_t                    =  0.1 0.1
> ref_t                    =  400 400
[...]
> #       System  RNA      SOL     Na      SOL_Na
>  200    269     405      266     504     266
[...]

> tc-grps                  =  RNA SOL Na
> tau_t                    =  0.1 0.1 0.1
> ref_t                    =  400 400 400
[...]
> #       System  RNA     SOL     Na      SOL_Na
>  200    268     248     268     350     268
[...]

I don't understand your results. You couple (in all cases) to 400K, 
while your system seems to be about 300K on average. You have 
'gen_vel=no', meaning you use starting velocities (if any) from your 
input structure file. Where did you get that from?

If you do not couple Na+ separately, and it remains bound to the RNA, it 
may not exchange heat enough with the water. This can explain the 
relative high T for your Na+ ions (and for the RNA).

> I use different time step and bond option for these 2 tests.
> And I use afm pulling options.
> I'm not sure whether these mdrun options will also influence the T-coupling.

Using 1fs timestep and no constraints vs. 2fs with constraints can 
already give different temperature behaviour, mainly due to more or less 
(roundoff) errors (which can heat), and the effect of constraints (which 
can cool).

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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