<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 15/06/2012 6:27 PM, Shima Arasteh wrote:
<blockquote
cite="mid:1339748843.50706.YahooMailNeo@web36401.mail.mud.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div><span>Thanks.</span></div>
<div><span>I read that it doesn't matter if the protein moves
and even protrudes the box. It's OK, but there is a question
here; why doesn't the box move rather than the protein? <br>
</span></div>
</div>
</blockquote>
<br>
The box could move, but it can't accelerate, else it wouldn't be an
<a href="http://en.wikipedia.org/wiki/Inertial_frame_of_reference">http://en.wikipedia.org/wiki/Inertial_frame_of_reference</a>.
I suspect the laws of motion necessary for the simulation to take
place in the frame of the (accelerating) motion of the protein COM
are more complex than those that take place in a simple inertial
frame. So that is not done - which also avoids having to force the
user to choose their inertial frame or GROMACS guessing what frame
they want.<br>
<br>
<blockquote
cite="mid:1339748843.50706.YahooMailNeo@web36401.mail.mud.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div><span>Is it possible for box to be defined every step?,
then the protein would stay in the center of the box.<br>
</span></div>
</div>
</blockquote>
<br>
The box is defined at every step. If you want your solute to have a
given relationship to the box every step you have to post-process
your trajectory as my earlier link told you.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1339748843.50706.YahooMailNeo@web36401.mail.mud.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div><span></span></div>
<div> </div>
<div>Sincerely,<br>
Shima<br>
</div>
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;">
<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>
Thursday, June 14, 2012 12:22 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] protein near the edges of simulation box<br>
</font> </div>
<br>
<div id="yiv1182153667">
<div> On 14/06/2012 5:47 PM, Shima Arasteh wrote:
<blockquote type="cite">
<div
style="color:#000;background-color:#fff;font-family:times
new roman, new york, times, serif;font-size:12pt;">
<div><span>Dear gmx friends,</span></div>
<div><br>
<span></span></div>
<div><span>I put a protein in a simulation box
filled of water molecules and entered the mdrun
command. After the simulation, I found the
protein near one of the edges of the box and not
in center. What is the problem? Anyone may
suggest me? <br>
</span></div>
<div><span>Does it mean that the simulation is
meaningless? <br>
</span></div>
<div><span>I expect the protein to stay in the
center of box and goes unfold by passing the
time.<br>
</span></div>
<br>
</div>
</blockquote>
See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><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>