[gmx-users] temperature using stochastic dynamics

[Berk Hess]

>Ahhhh, I think that's the problem.  I naively assumed that tau_t was the
>parameter that controlled the viscosity in langevin equation, based on what
>I had read in the manual.  But now I see that it acts the same as the weak
>temperature coupling.  So, I was looking in the manual to make sure
>I understand how to control the viscosity and the temperature coupling, but
>it wasn't clear to me what is going on.  Could someone let me know if I
>understand this correctly?  Suppose I want to run my experiment at 300K,
>I should set ref_t=300 and tau_t at a low value, saw 0.2 as Alessandra
>suggested.  Then suppose I want to run the simulation with a viscosity of 
>1.0
>ps^-1, I should set bd_fric=1?  Is this right?  It isn't obvious to me that 
>a
>Brownian Dynamics parameter would also control a Stochastic Dynamics
>parameter since they are different integrators.  Please clarify this for 
>me?
>Thanks.
>
>Sid

As stated in the manual, the inverse friction constant for each group is set 
with
tau_t. If your temperature is 255 K instead of 300 K, some very non-linear
things are happening. This usually means your time-step is quite large.
What kind of system are you simulating with what kind of time step?

Berk.







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