[gmx-users] Question about "compressibility" in P-coupling and "Berendsen" in T-coupling
Mark.Abraham at anu.edu.au
Thu Oct 8 23:57:00 CEST 2009
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
> What does this note mean? For my system (protein + solvent), will
> the choice of different T-coupling method be very different for dynamic
Perhaps... see section 3.4.5 in the first instance.
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