After bringing the system's temperature to a stable range of around 300K, we will now use a barostat in combination with the thermostat to model the system with an environment that closely resembles the experimental conditions. In the second step equilibration, we will run the NPT ensemble run for 500 ps with a V-rescale thermostat, weakly-coupled Berendsen barostat and position restraints for heavy atoms. Note that we implement semi-isotropic pressure coupling to separate the way the fibril feels pressure along the chain axis (Z) and the other two axes. The pressure coupling is isotropic in the X and Y direction.
; Pressure coupling
pcoupl = Berendsen ;Parrinello-Rahman for production run (NPT)
pcoupltype = semiisotropic ; uniform scaling of box vectors in x-y and independent z
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
Note that the default vdw radii value of “0.57” is meant for a density of 1 g/cm3 for water, but here we will use a “0.48” radii value to obtain ~0.85 g/cm3 density.
Important: In practice, the size of the large box is decided by a trial-and-error approach until we find the box size that fits the target polymer chain count. This approach is based on the study by Lemkul. JA et.al.