<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 28/01/2011 4:25 AM, WU Yanbin wrote:
<blockquote
cite="mid:AANLkTikqeFnAf_X3UHb8A=s3Je1NZ_iLi=-8Pp3agWjQ@mail.gmail.com"
type="cite">Dear GMXers,<br>
<br>
I would like to reproduce the water droplet contact angle on
graphite surface, as in Werder, T.; Walther, J. H.; Halicioglu,
T.; Koumoutsakos, P. <i>J. Phys. Chem. B</i> <b>2003</b>, <i>107</i>,
1345-1352.<br>
<br>
The box size is 20nm by 20nm by 30nm. Graphite is represented by a
two-layer carbon sheet. After equilibration, the water droplet is
around 3.5nm in radius. A large part of the box is vacuum.
Periodic boundary condition (PBC) is applied. Graphite is fixed
throughout the simulation.<br>
</blockquote>
<br>
I'm not sure what PBC is gaining for you. I think you want vacuum
boundary conditions, which may as well be non-periodic.<br>
<br>
<blockquote
cite="mid:AANLkTikqeFnAf_X3UHb8A=s3Je1NZ_iLi=-8Pp3agWjQ@mail.gmail.com"
type="cite">
<br>
From the manual, the "comm_mode=Linear" option should be applied,
which means the translational motion of the center of mass of the
water droplet should be removed. My first question is: If the time
step is 2fs, what's the recommended value for nstcomm? (nstlist is
updated very 3 time step)<br>
</blockquote>
<br>
10 is probably fine.<br>
<br>
<blockquote
cite="mid:AANLkTikqeFnAf_X3UHb8A=s3Je1NZ_iLi=-8Pp3agWjQ@mail.gmail.com"
type="cite">
<br>
Also in the manual and this mail list, it's mentioned that for
non-PBC, isolated system, "comm_mode=Angular" should be applied.
Does this also applied to my partial filled PBC box?<br>
</blockquote>
<br>
No, this is referring to simulations like a protein in vacuum.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTikqeFnAf_X3UHb8A=s3Je1NZ_iLi=-8Pp3agWjQ@mail.gmail.com"
type="cite">Do let me know if the question is not clear.<br>
<br>
Thank you.<br>
<br>
Best,<br>
Yanbin<br>
</blockquote>
<br>
</body>
</html>