[gmx-users] temperature using stochastic dynamics

[Sidney Elmer]

Alessandra Villa wrote:

> On Thu, 14 Nov 2002, Sidney Elmer wrote:
>
> > Hi,
> >
> > When I run stochastic dynamics (integrator=sd) at 300K (ref_t=300.0) the
> > actual simulation temperature fluctuates around an average value ~255.0K
> > (rmsd ~60K).  Did I miss a conversion factor for temperature, or
> > something?  I don't understand what's going on.  Thanks a bunch.
> >
> > Sid
>
> Maybe you are not using the correct tau_t (inverse of  friction)
> I usually use  tau_t = 0.2 and for small molecules in water in ok.
>
> Best
> Alessandra
>
> >
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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