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<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman"">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";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman""> in
Sugita and Okamoto publication, 1999</span><span style="font-size:12.0pt;
font-family:"Times New Roman","serif";mso-fareast-font-family:"Times New Roman"">).
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="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman"">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="MsoNormal" 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="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></p><p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
</p><p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman"">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="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman"">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="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";"><span style="mso-spacerun:yes"></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="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">Thanks,</span></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman"">Michael<br></span></p>
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