<font color="#000099"><font face="verdana,sans-serif">Thanks. Actually I applied just because the tutorial said so :(</font></font><div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :(</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">I am totally fresh to MD simulation, just worked on this for 1 week ...<br></font></font><br>
<div class="gmail_quote">On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 30/09/2011 2:50 AM, Liu, Liang wrote:
<blockquote 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></div>
Yep. One for each simulation.<div class="im"><br>
<br>
<blockquote 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></div>
Justin told you yesterday they would not be, because you have made a
number of totally arbitrary choices.<div class="im"><br>
<br>
<blockquote 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 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></div>
Why did you want to demux?<div class="im"><br>
<br>
<blockquote 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></div>
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><font color="#888888">
<br>
Mark<br>
</font></div>
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</div>