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On 22/02/2012 3:11 AM, mohammad agha wrote:
<blockquote
cite="mid:1329840694.95617.YahooMailNeo@web125701.mail.ne1.yahoo.com"
type="cite">
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font-size: 14pt;">
<div>Dear Gromacs Specialists,</div>
<div><br>
</div>
<div>I made a box consists of water with box lengths: 6nm *
6nm * 6nm , then I equilibrated it with NPT ensemble, box
size increased to 6.66176, then I <font face="Arial"><font
size="3">kept the <i>x-</i> and <i>y-</i>dimensions
fixed, and double the system size in <i>z as following:</i></font></font></div>
<div><font face="Arial"><font size="3"><i>editconf -f pr1.gro -o
newbox1.gro -box 6.66176 6.66176 13.32352 -center
3.33088 3.33088 3.33088<br>
Next that, I placed one surfactant in center of water
phase as following:</i></font></font></div>
<div><font face="Arial"><font size="3"><i>editconf -f
surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176
13.32352 -center 3.33088 3.33088 1.66544<br>
genbox -cp newbox-cta.gro -cs newbox1.gro -o newbox2.gro</i></font></font></div>
<div><font face="Arial"><font size="3"><i>and I added one ion to
my system, then ran md.mdp for production simulation. <br>
</i></font></font></div>
<div><font face="Arial"><font size="3"><i>Do I have one
air/water interface in my system?</i></font></font></div>
</div>
</blockquote>
<br>
You need to use visualization software and see if the configuration
looks like you intend it to look. You certainly don't have an
air-water interface if one of them is vacuum.<br>
<br>
Mark<br>
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