Re: Barostat dimension rescaling under semi-isotropic pressure coupling conditions

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Mon Sep 16 2019 - 17:24:41 CDT

> In an NPT simulation with semi-isotropic pressure coupling, how does the barostat scale the dimensions of the box?

The details are in the paper:

GJ Martyna, DJ Tobias and ML Klein, "Constant pressure molecular dynamics algorithms", J. Chem. Phys 101(5), 1994
SE Feller, Y Zhang, RW Pastor and BR Brooks, "Constant pressure molecular dynamics simulation: The Langevin piston method", J. Chem. Phys. 103(11), 1995.

> In particular, since pressure is supposed to be constant and equal to the target pressure in z, would the barostat scale predominantly the z-dimension of the box?Or would it scale all dimensions equally?

From NAMD manual:

useFlexibleCell [$ <$] anisotropic cell fluctuations [$ >$]
Acceptable Values: yes or no
Default Value: no
Description: NAMD allows the three orthogonal dimensions of the periodic cell to fluctuate independently when this option is enabled.

In the case of isotropic pressure coupling, the scalar pressure (trace(P)/3) is used in place of the pressure tensor.

> The x and y dimensions should change the same way (due to the semi-isotopic coupling) but how is that achieved?

Looking at your publication record, I assume you are interested in simulation of membranes. You are probably looking for this.

useConstantArea [$ <$] constant area and normal pressure conditions [$ >$]
Acceptable Values: yes or no
Default Value: no
Description: When enabled, NAMD keeps the dimension of the unit cell in the x-y plane constant while allowing fluctuations along the z axis. This is not currently implemented in Berendsen's method.


On Mon, Sep 16, 2019 at 5:57 PM Milka Doktorova <milka.doktorova_at_gmail.com<mailto:milka.doktorova_at_gmail.com>> wrote:
Hi,

In an NPT simulation with semi-isotropic pressure coupling, how does the barostat scale the dimensions of the box? In particular, since pressure is supposed to be constant and equal to the target pressure in z, would the barostat scale predominantly the z-dimension of the box? Or would it scale all dimensions equally? The x and y dimensions should change the same way (due to the semi-isotopic coupling) but how is that achieved?

Thank you.
Milka

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:50 CST