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On 18/09/2011 9:35 PM, michael zhenin wrote:
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cite="mid:CAHGgLDN+32i+88_mjAbFdsO-WBew51BaD0vAR9LjVNRip=4sTQ@mail.gmail.com"
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<p class="MsoNormal" style="margin-bottom: 0.0001pt;
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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: 12pt; font-family: "Times New
Roman","serif";">).</span></p>
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<br>
As Sebatian noted, in GROMACS the replicas move between simulations
and the temperature of each simulation is constant. You will see
this in the temperatures in the .log files. This approach is
conceptually identical, of course, but there are advantages for
doing one or the other when writing the code.<br>
<br>
<blockquote
cite="mid:CAHGgLDN+32i+88_mjAbFdsO-WBew51BaD0vAR9LjVNRip=4sTQ@mail.gmail.com"
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Roman","serif";mso-fareast-font-family:"Times
New Roman"">
Then <a moz-do-not-send="true" 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>
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<br>
They are already present in the lowest-numbered replica trajectory.
Using demux.pl will be counter-productive - it generates
geometrically continuous trajectories from ensemble-continuous
trajectories (and vice versa, I think).<br>
<br>
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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""> </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>
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<br>
That's consistent with GROMACS REMD simulating a constant ensemble.
You can't do demux on the energy files in the current
implementation.<br>
<br>
Mark<br>
<br>
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<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 moz-do-not-send="true"
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;
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<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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