mateusz sikora wrote:
Hi all,
i am trying to set up high pressure simulations of a protein. I am using
NPT ensemble, with isotropic pressure scaling, standard compressibility,
room temperature. I am wondering how I can rise pressure from 1 bar to
as much as 5 kBar. Is it safe to do it under Parinello-Raman coupling? I
want to avoid huge oscillations of a box while adding the pressure -
they can result in a box explosion/collapse. Would setting tau_P to some
bigger value (like 100 or something) make any difference?
Changing tau_p will damp the extent to which the coupling affects the
system. You should probably do this process with stepwise increments of
ref_p. You should also go and parameterize a force field for high
pressures, too, since the standard ones are parameterized against
experimental data from 1 bar or so. There's no reason to suppose the
parameters are transferable to high pressure, unless you can demonstrate
that they are by comparison of simulation and suitable experimental data.
Mark
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