<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 22/02/2012 10:34 PM, mohammad agha wrote:
<blockquote
cite="mid:1329910468.65276.YahooMailNeo@web125706.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: bookman old style,new york,times,serif;
font-size: 14pt;">
<div><span>Dear Mark,</span></div>
<div><br>
<span></span></div>
<div><span>Thank you very much from your reply.</span></div>
<div><span>I see a box that the half of it consists of water and
another half of box is void, but when I run md.mdp for
production simulation all of water molecules dispersed in
total of box and I don't see interface and total of box
filled by water.</span></div>
</div>
</blockquote>
<br>
What did you expect a liquid in contact with a vacuum to do?<br>
<br>
<blockquote
cite="mid:1329910468.65276.YahooMailNeo@web125706.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: bookman old style,new york,times,serif;
font-size: 14pt;">
<div><br>
<span></span></div>
<div><span>Can you help me to construct the air/water interface,
Please?</span></div>
</div>
</blockquote>
<br>
First you need to decide how you're going to produce a valid model
of *air* which is different from a *vacuum*. Then you need to find
parameters for such a model. Then it's the same kind of approach as
a mixed-solvent system (see gromacs webpage), only here it will be
mixed fluid.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1329910468.65276.YahooMailNeo@web125706.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:bookman
old style, new york, times, serif;font-size:14pt">
<div><span><br>
</span></div>
<div><span>Best Regards</span></div>
<div><span>Sara</span></div>
<div><br>
</div>
<div style="font-family: bookman old style, new york, times,
serif; font-size: 14pt;">
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;">
<div dir="ltr"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Wednesday, February 22, 2012 12:59 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] interface<br>
</font> </div>
<br>
<div id="yiv1653808336">
<div> On 22/02/2012 3:11 AM, mohammad agha wrote:
<blockquote type="cite">
<div style="color:rgb(0, 0,
0);background-color:rgb(255, 255,
255);font-family:bookman old style, new york, times,
serif;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>
</div>
</div>
<br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the <br>
www interface or send it to <a moz-do-not-send="true"
ymailto="mailto:gmx-users-request@gromacs.org"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>