[gmx-users] high pressure simulations

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 15 14:17:55 CET 2007

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.


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