[gmx-users] Unreasonably high pressure values

Kamps, M. m.kamps at student.rug.nl
Tue May 16 11:34:24 CEST 2017

Dear Mark,

I'm sorry for being unclear. I have rectangular box (20x5x7 nm, XYZ)
where a flow should be replicated. at Z=0 and Z=7 there are two
surfaces composed of gold atoms. In between there is a fluid. The
system is open or periodic in the X and Y directions, but limited in
the Z direction by the surfaces (PBC is set to XYZ, while periodic
molecules is set to yes). Both surfaces 'connect' through the PBC. The
goal is to replicate a fluid flow between the two surfaces, which will
by done by applying a constant acceleration to the fluid in the X
direction. The flow will be therefore along the X axis. It is somewhat
similar to articles as these:

I don't fully understand what you mean in your last sentences. Why
shouldn't my system produce sane values of pressure?


Message: 1
Date: Tue, 16 May 2017 09:11:46 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Unreasonably high pressure values
        <CAMNuMAQgsC4yNNvAT09mz=FEcV9=TGajE-gbgtLaABzpriCeoA at mail.gmail.com>
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I don't understand the system very well from your description. You have two
surfaces, a fluid between them, presumably periodic in the dimensions of
the surface. But what do you have in the direction normal to the surface?
Whatever it is, why should your parameterization of your gold atoms LJ lead
to sane pressure? What do you get from a normal 3D periodic system with a
surface solvated on both sides?


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