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Berk Hess wrote:
<blockquote cite="midBAY110-F24E6B0042DCA8903295C2B8E1D0@phx.gbl"
type="cite"><br>
<br>
<br>
<blockquote type="cite">From: Matteo Guglielmi
<a class="moz-txt-link-rfc2396E" href="mailto:matteo.guglielmi@epfl.ch"><matteo.guglielmi@epfl.ch></a>
<br>
Reply-To: Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
<br>
To: GMX-LIST <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
<br>
Subject: [gmx-users] Anisotropic Pressure
<br>
Date: Fri, 15 Jun 2007 19:11:50 +0200
<br>
<br>
Hello Folks,
<br>
<br>
Is there any difference between these two anisotropic pressure setup?
<br>
<br>
### 1st setup ###
<br>
<br>
pcoupl = berendsen
<br>
pcoupltype = anisotropic
<br>
tau_p = 5.0 5.0 5.0 0.0 0.0 0.0
<br>
compressibility = 4.53e-5 4.53e-5 4.53e-5 0.0 0.0 0.0
<br>
ref_p = 1.025 1.025 1.025 0.0 0.0 0.0
<br>
<br>
<br>
### 2nd setup ###
<br>
<br>
pcoupl = berendsen
<br>
pcoupltype = anisotropic
<br>
tau_p = 5.0 5.0 5.0 5.0 5.0 5.0
<br>
compressibility = 4.53e-5 4.53e-5 4.53e-5 0.0 0.0
0.0
<br>
ref_p = 1.025 1.025 1.025 1.025 1.025
1.025
<br>
<br>
</blockquote>
<br>
If the compressibility is zero, the corresponding unit-cell degree of
freedom
<br>
will not change, so effectively there is no difference.
<br>
<br>
<blockquote type="cite"><br>
Which one would you suggest for anisotropic coupling (solvated pore
<br>
immersed into a membrane)
<br>
</blockquote>
<br>
Neither, you should probably use surface-tension coupling.
<br>
<br>
Berk.
<br>
<br>
</blockquote>
Ok, thanks for the answer.<br>
<br>
Actually I never used surface-tension coupling but the manual says:<br>
<br>
"Surface tension coupling for surfaces parallel to the xy-plane."<br>
<br>
... which is my case.<br>
<br>
"Uses normal pressure coupling for the z-direction, while the surface<br>
tension is coupled to the x/y dimensions of the box."<br>
<br>
Ok.<br>
<br>
"The first ref_p value is the reference surface tension times the number<br>
of surfaces [bar nm],"<br>
<br>
I have a lipid bilayer membrane su I guess I should multiply by 2 the<br>
surface tension value for which I do not have any guess about its value.<br>
<br>
"the second value is the reference z-pressure [bar]."<br>
<br>
Ok... I could use the default value (<b>phosphatidylethanolamine</b>
membrane<br>
in water).<br>
<br>
"The two compressibility [bar−1] values are the compressibility in the
x/y<br>
and z direction respectively."<br>
<br>
What about the first one?<br>
For the z direction I could use the water compressibility...<br>
<br>
"The value for the z-compressibility should be reasonably accurate
since it<br>
influences the convergence of the surface-tension, it can also be set
to zero<br>
to have a box with constant height."<br>
<br>
Any suggestion on how I could complete the surface tension coupling set
up?<br>
<br>
<br>
MG.<br>
<br>
<br>
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