<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: x-small;">
<pre>Dear Hugh:</pre>
<pre><br></pre>
<pre>I can't answer your question, but I can address the error message that you see.</pre>
<pre>Basically, your semi-isotropic pressure coupling allows the surface area of the water-decane</pre>
<pre>interface to get smaller as z increases and x and y decrease. In a system with only water</pre>
<pre>and decane, this will continue until you have a single file of decane aligned in z.</pre>
<pre>To avoid this, you need to use semi-isotropic pressure coupling but set the compressibility </pre>
<pre>to zero in the z dimension (or, alternatively set the compressibility to zero in both x and y).</pre>
<pre>This will get rid of the error message, as I see that you have already noted.</pre>
<pre>So I guess that all I can tell you is that your first option is not going to be possible and</pre>
<pre>that your second option is giving you the wrong value because your surfactants are fighting the</pre>
<pre>elongation of your box along z, but the effect persists.</pre>
<pre><br></pre>
<pre>Chris.</pre>
<pre><br></pre>
<pre>-- original message --</pre>
<pre><br></pre>
<pre>Dear Gromacs users,
I have do simulation of surfactant at oil/water interface for a long time.
But I find it too difficult to get a reasonable interfacial tension. The
key question is the pcoupltype.
My system:
Box size: 3.0 * 3.0 * 13
><i> Molecule Number: decane 230, water 2041
</i>><i> pcoupltype = semiisotropic
</i>
Gromacs version: 4.5.5
1. When I set compressibility = 4.5e-5 4.5e-5. Surfactant number is 32
. The box will be shrink at x and y. At last simualion will end for a fatal
error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS.
2. When I add the number of surfactants to 40. compressibility = 4.5e-5
4.5e-5. The interfacial tension is -20bar/nm for two interfaces. It is not
reasonable because it should be positive.
3. When I compressibility = 0 4.5e-5. Surfactant number is 32. The
interfacial tension is 794bar/nm for two interfaces.
My question is:
What is the right way to simulate for this system? My work confused me too
much. Very appreciate for you help.
Hugh</pre>
</div>
</body>
</html>