[gmx-users] high pressure simulations

[Mark Abraham]

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