[gmx-users] temperature using stochastic dynamics
sidnasty at stanford.edu
Fri Nov 15 19:31:13 CET 2002
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.
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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?
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