[gmx-users] strange temperature coupling problem

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 13 05:51:48 CET 2006

Simple wrote:
> Nickle Fan writed:
>>Dear Gromacs users:
>>I am having a rather strange problem in one of my simulation. The system
>>consists of 2000 water molecules embedded between two walls. The wall atoms
>>are position restrainted (force constant: 5000).
>>The system is first equiliburated under NVT (Berendsen thermostat, tau_t =
>>0.1ps, Tsystem = 300K) for a while. Then I coupled the wall atoms to 300K
>>(tau_t = 0.1 ps), and water to 300K (tau_t = 3000 ps). I found that during
> I found you used (tau_t = 3000 ps) for water, I don't know why you use 
> different tau_t for wall and water.But I think, under your setting, the 
> temperature will only couple at  3000 ps interval. So in a 100ps simulation, 
> the temperature of water would never adjust,Then the increasing of temp seem 
> reasonable.
> I'm not familiar with this problem.I only notice the strange setting, maybe 
> there are other opinions, 

3000ps is an extremely large coupling constant to want to use.

In any case, "Simple" is wrong about the frequency of coupling. This 
coupling constant is a parameter in an algorithm that is applied each 
step that expresses how well-connected the group is to the thermal 
reservoir. It is not a time interval between applications of the algorithm.

I suggest you both have a read of section 3.4.5 of the gromacs manual, 
where it will tell you that "The Berendsen algorithm is stable up to 
Delta T approx tau_t". Doubtless 3000ps is much larger than your 
simulation timestep, and the instability is not surprising!


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