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Dear Michael,<div><br></div><div>First I want to say thank you very much... for posting you questions here.<br>I can't help you with this but I wish you Good Luck and that you will find your answers soon!</div><div><br></div><div>Best wishes,</div><div>thanks again,</div><div><br></div><div>Gal :)</div><div><br></div><div><br><div><hr id="stopSpelling">Date: Sun, 18 Sep 2011 14:35:43 +0300<br>From: mikelj25@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Questions regarding REMD simulation<br><br><div dir="rtl"><div dir="ltr">
<p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Hi All,<br>
<br>
I have few questions regarding REMD simulation.<br>
<br>
I assume REMD works in the following way: Each replica starts with a given
temperature and the temperature of each replica changes along the
simulation (as described</span><span style="font-size:12.0pt;font-family:"CMR12","serif""> in
Sugita and Okamoto publication, 1999</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">).
Then <a href="http://demux.pl/" target="_blank"><span style="color:blue">demux.pl</span></a>
and trjcat collect the trajectories of the lowest temperature from
each replica.</span></p>
<p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">My problem is that while analyzing
the results, I found in the edr files that the temperatures along
each replica are relatively</span></p>
<p class="ecxMsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"">constant (+- 2K from the
starting temperature) and the average temperature is equal to the initial
temperature.</span></p><p class="ecxMsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><br><span style="font-size:12pt;font-family:"Times New Roman","serif""></span></p><p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal">
</p><p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">How can this be explained? Does the
temperature of each replica change along the simulation
or maybe the temperature of each </span></p>
<p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">simulation stays close
to its initial value and the coordinates are changed between the different
replica? (if so, why do i need to use </span></p>
<p class="ecxMsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif""><span style=""></span>the post-processing tools such as the <a href="http://demux.pl/" target="_blank"><span style="color:blue">demux.pl</span></a>
script?)</span></p><p class="ecxMsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><br><span style="font-size:12pt;font-family:"Times New Roman","serif""></span></p><p class="ecxMsoNormal" style="margin-bottom:0.0001pt;line-height:normal">
<span style="font-size:12pt;font-family:"Times New Roman","serif"">Thanks,</span></p><p class="ecxMsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><br><span style="font-size:12pt;font-family:"Times New Roman","serif""></span></p>
<p class="ecxMsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Michael<br></span></p>
</div></div>
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