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
compressibility?
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?
Thanks in advance.
--
Sincerely
=================================
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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