<font color="#000099"><font face="verdana,sans-serif">Yes, they are updated like:</font></font><div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif">...<br></font><div><font color="#000099"><font face="verdana,sans-serif"><div>
Replica exchange at step 5700 time 11.4</div><div>Repl ex 0 1 x 2 3 x 4 5 x 6 7 8 9 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49</div>
<div>Repl pr 1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00</div>
<div><br></div><div>Replica exchange at step 5750 time 11.5</div><div>Repl 0 <-> 1 dE = -7.583e+00</div><div>Repl ex 0 x 1 2 3 4 x 5 6 x 7 8 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49</div>
<div>Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01</div>
<div><br></div><div> Step Time Lambda</div><div> 5800 11.60000 0.00000</div><div><br></div><div> Energies (kJ/mol)</div><div> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14</div>
<div> 9.69806e+02 1.32207e+03 3.34938e+01 4.93171e+02 -3.91111e+03</div><div> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.</div><div> 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.00000e+00</div>
<div> Potential Kinetic En. Total Energy Conserved En. Temperature</div><div> -1.78987e+05 4.57462e+04 -1.33240e+05 1.23302e+10 5.62201e+02</div><div> Pres. DC (bar) Pressure (bar) Constr. rmsd</div>
<div> -2.12803e+02 -5.47109e+02 2.21484e-05</div><div>...</div></font></font><br><div class="gmail_quote">On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running?<br>
<br>
</blockquote>
<br></div>
Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Liu, Liang wrote:<br>
<br>
Well, although this makes sense, why all the 50 replicas are<br>
running when I run "mpirun<br>
-np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own<br>
computer with only 2 cores?<br>
<br>
<br>
I can offer no explanation for this behavior, but I expect that<br>
either not all of them are actually running, or at the very least<br>
you will get horribly slow performance.<br>
<br>
<br>
By the way, would you please show me where I can find the<br>
reasonable replex number information in the literature? I did<br>
not find it in the link you posted and the manual either.<br>
<br>
<br>
A few minutes of real literature searching will be far more valuable<br>
than some random person on the Internet giving you a value that you<br>
blindly use ;)<br>
<br>
-Justin<br>
<br>
Thanks.<br>
<br>
<br>
-- Best,<br>
Liang Liu<br>
<br>
<br>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
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-- <br>
Best,<br>
Liang Liu<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>
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