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

Pan Wu pan.wu at duke.edu
Thu Oct 8 23:19:04 CEST 2009

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:
            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

    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 results?

    Thanks in advance.

Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
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