[gmx-users] Question about "compressibility" in P-coupling and "Berendsen" in T-coupling

[Mark Abraham]

Pan Wu wrote:
> Hello gmx users, 
> 
>     I am trying to simulate one protein in solvent with PBC xyz in 
> standard condition (1 atm, 303K). However since I am using Martini 
> force-field, some parameters in P-coupling and T-coupling confuse me a 
> lot. Here are two questions listed below:
>     1. What is the compressibility mean? In my simulation can I just use:

See section 3.4.6. In general, there's background information earlier in 
the manual for things in section 7.3.

>             Pcoupl = Berendsen
>             Pcoupletype = isotropic
>             tau_p = 2.0
>             compressibility = 4.5e-5
>             ref_p = 1.0
>         However, in the Gromacs 4.0 manual, it shows "For water at 1 atm 
> and 300 K the compressibility is 4.5e-5 [bar-1]", does it mean I don't 
> have to consider about coarse-grained water molecule difference when 
> setting the compressibility?

It might, but that advice was neither for coarse-grained simulations in 
general nor Martini in particular. You should probably follow examples / 
advice from its literature, before that for general GROMACS.

>     2. For T-coupling, I use "Berendsen" method. After generating the 
> job, there is one note:
>         "The Berendsen thermostat does not generate the correct kinetic 
> energy distribution. You might want to consider using the V-rescale 
> thermostat."
>       What does this note mean? For my system (protein + solvent), will 
> the choice of different T-coupling method be very different for dynamic 
> results?

Perhaps... see section 3.4.5 in the first instance.

Mark