<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 30/09/2011 2:50 AM, Liu, Liang wrote:
<blockquote
cite="mid:CABxJRoK327L+b3DfF-ihz5n7FgNgeojA1wJKBTLS2krxBV7ibA@mail.gmail.com"
type="cite"><font color="#000099" face="verdana, sans-serif"><span
style="color: rgb(0, 0, 0); font-family: arial,sans-serif;
font-size: 13px; background-color: rgb(255, 255, 255);"><font
color="#000099"><font face="verdana,sans-serif">After
running for more than 12 hours, the REMD simulation is
completed and what I get is 50 log, 50 trr, 50 cpt and 50
tpr files.</font></font></span></font></blockquote>
<br>
Yep. One for each simulation.<br>
<br>
<blockquote
cite="mid:CABxJRoK327L+b3DfF-ihz5n7FgNgeojA1wJKBTLS2krxBV7ibA@mail.gmail.com"
type="cite"><font color="#000099" face="verdana, sans-serif"><span
style="color: rgb(0, 0, 0); font-family: arial,sans-serif;
font-size: 13px; background-color: rgb(255, 255, 255);">
<div>
<font color="#000099"><font face="verdana,sans-serif">Not
sure if the result is reasonable.</font></font></div>
</span></font></blockquote>
<br>
Justin told you yesterday they would not be, because you have made a
number of totally arbitrary choices.<br>
<br>
<blockquote
cite="mid:CABxJRoK327L+b3DfF-ihz5n7FgNgeojA1wJKBTLS2krxBV7ibA@mail.gmail.com"
type="cite"><font color="#000099" face="verdana, sans-serif"><span
style="color: rgb(0, 0, 0); font-family: arial,sans-serif;
font-size: 13px; background-color: rgb(255, 255, 255);">
<div><font color="#000099"><font face="verdana,sans-serif">I
tried to analyze the result, and after applying <a
moz-do-not-send="true" href="http://demux.pl/"
style="color:rgb(66, 99, 171)" target="_blank">demux.pl</a>,
two files replica_index.xvg replica_temp.xvg are
obtained.</font></font></div>
</span></font></blockquote>
<br>
Why did you want to demux?<br>
<br>
<blockquote
cite="mid:CABxJRoK327L+b3DfF-ihz5n7FgNgeojA1wJKBTLS2krxBV7ibA@mail.gmail.com"
type="cite"><font color="#000099" face="verdana, sans-serif"><span
style="color: rgb(0, 0, 0); font-family: arial,sans-serif;
font-size: 13px; background-color: rgb(255, 255, 255);">
<div><font color="#000099"><font face="verdana,sans-serif">My
question is how to obtain the structure information? (I
will need pdb file).</font></font></div>
</span></font></blockquote>
<br>
Do all the tutorial material you can find - even if not strictly
relevant - to get an idea about good workflows. Then try to
replicate (part of) a published REMD study to see how things work
there. Search the web and check out the GROMACS web page - there's
lots of material out there. Stabbing in the dark is a great way to
waste your time, and people here don't have the time to teach every
person every thing.<br>
<br>
Mark<br>
</body>
</html>