[gmx-users] Question about nsttcouple

[Justin Lemkul]

On 11/7/18 9:43 AM, minky son wrote:
> Dear gmx users,
>
>
> In gromacs manual,
>
> “nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
> unless nstlist <=0, then a value of 10 is used.”
>
>
>
> When I did grompp with the following mdp options,
>
> nstlist = 20
>
> tcoupl = berendsen
>
> nsttcouple = -1
>
> tau-t = 0.1
>
>
>
> I got a warning message.
>
> WARNING 1 [file pr_nvt.mdp]:
>
>    "For proper integration of the Berendsen thermostat, tau-t (0.1) should
> be at least 5 times larger than nsttcouple*dt (0.04)"
>
>
>
> I think this means that nsttcouple is applied to 20, not 10. This doesn't
> match with the one mentioned in the manual. why?

It does match the manual, it's just grammatically complicated. A value 
of 10 is used for nstlist if *both* nsttcouple = -1 and nstlist <= 0. 
You have nstlist = 20, so the presence of nsttcouple = -1 means it is 
set to 20, not 10.

>
>
>
> When I also tried nstlist=10, grompp didn’t show any warning.

Because now nsttcouple*dt is 0.02 (assuming dt = 0.002), and your tau-t 
is, in fact, 5 times larger.

> But the value of nstlist was automatically changed to 40 in mdrun.

mdrun always tunes this with the Verlet algorithm.

> Is nsttcouple applied to 10 in this case?

Check your .log file.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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