[gmx-users] Re: Temperature coupling problem: reference T is different to given T in mdp file

Andrey Frolov andrey.i.frolov at mail.ru
Tue Jan 22 15:27:01 CET 2013

Dear Justin,

> Considering all data points will include early frames that are not
> necessarily 
>anywhere close to being equilibrated.  You could try block averaging to see
>the results converge to the correct result over the latter part of the 
>simulation, or at least see if the system is approaching the target

Temperature jumps to the "wrong" target temperature at the beginning of the
simulation (see the figure attached). So, this is not the reason of the


> It would be better to diagnose the system using PME.  Even if the results
> are 
> "similar," rounding errors are compounded when using plain cutoffs, which
> render 
> the results inherently unreliable.

This is true. But, the problem persists even with PME. I have simulations
with slightly different setup: more CO2 molecules and higher CO2
concentration, umbrella windows for different separations between
paracetamol molecules, 24 ns simulation time, with PME electrostatics. Here
it gives me the "wrong" average temperature 478.486 K, while i set v-rescale
thermostat to 423.15 K. So, electrostatics method seems to play no role in

Moreover, i tested the same simulation setups as in the initial posts with
Nose-Hoover thermostat. Single Nose-Hoover with number of chains = 1 gives
correct temperatures (the same as a set in mdp file). Even if i set three
thermostats to three subsystems (eventhough, i agree that this approach is
valid only for testing purposes) the resulting temperatures are correct.

But with N chains = 10, the resulting temperatures are again wrong (up to ~
20 K). (In this case integrator was md-vv).


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