Hi Justin<br><br>Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can.<br><br>Thanks,<br>Sapna<br><br><div class="gmail_quote">On Tue, Aug 17, 2010 at 5:36 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
sapna sarupria wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Justin<br>
Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)?<br>
</blockquote>
<br></div>
There is no way to limit PME to certain ranges. Â It is a method for solving infinite sums. Â Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. Â You may want to see how others (in the literature) deal with droplet-type simulations.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
Thanks for your help.<br>
<br>
Sapna<br>
<br></div><div><div></div><div class="h5">
On Tue, Aug 17, 2010 at 5:29 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>
  sapna sarupria wrote:<br>
<br>
    Hi all,<br>
<br>
    I am running (NVT) simulations of a drop of water (~5 nm in<br>
    radius) in a big box (~25 nm) in a box and find that the<br>
    simulations are rather slow. I am getting about 0.8 ns per day<br>
    when a simulation of bulk system of equivalent number of waters<br>
    will be much faster. The number of waters is ~12000. I was<br>
    wondering if anyone can suggest methods with which I can speed<br>
    up the simulations. I am using domain decomposition and<br>
    optimize_fft is set to yes. PME is used for the electrostatics.<br>
<br>
<br>
  I would suspect that the lag comes from a lot of unused PME<br>
  calculations. During your run, PME grid points will be assigned to<br>
  vacuum space, for which nothing needs to be done.  You can check<br>
  imbalances and performance loss in the log file.<br>
<br>
  -Justin<br>
<br>
<br>
    Thank you<br>
<br>
    Sincerely<br>
    Sapna<br>
<br>
<br>
  --   ========================================<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>
  jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
  <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
<br>
<br>
-- <br>
Sapna Sarupria<br>
Post-doctoral Researcher<br>
Princeton University<br>
New Jersey 08540<br>
U.S.A.<br>
<br>
Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw.<br>
Dare to Dream<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Sapna Sarupria<br>Post-doctoral Researcher<br>Princeton University<br>New Jersey 08540<br>U.S.A.<br><br>Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. <br>
Dare to Dream<br>