[gmx-users] different ref_t

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Jun 29 16:45:37 CEST 2010

Can you please supply gen_temp and also your pressure coupling values?  
Also, please supply the g_energy values that show the temperatures  
changing as you suggest (with accompanying timestep info).

I'm fairly sure that what is happening is that you are simply seeing  
the nose-hoover oscillations (possibly coupled to your pressure  
coupling fluctuations) and since your CHCl3 is presumably very small  
then you see a larger effect on it.

I'd suggest doing a few tests: 1. Increase tau_t to 0.1 or perhaps 0.4  
(I don't use nose-hoover, but your value seems small). 2. Run longer  
and see if it is indeed a fluctuation and not just a trend to zero. 3.  
Why not try the SD integrator?

And a PS that I'm simply assuming that you know what you're doing with  
2 different temperatures since you didn't ask for advice on that part.


-- original message --

I try to simulate a small peptide in CHCl3 there the
peptide is couplet to a heat bath at a different

tcoupl              =  nose-hoover
tc-grps             =  Protein+PTS+AIC CHCl3
tau_t               =  0.01 0.01
ref_t               =  220  300

If I do so the temperature of the CHCl3 molecules drop down
to almost 0K and the temperature of the peptide increases
significantly. Has someone any experience with such a
system and can give me a hint what to do?

Thanks a lot

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