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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
