That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is.<br>
<br><div class="gmail_quote">On Wed, Aug 18, 2010 at 10:26 AM, ms <span dir="ltr"><<a href="mailto:devicerandom@gmail.com">devicerandom@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 17/08/10 22:36, Justin A. Lemkul wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
There is no way to limit PME to certain ranges. It is a method for<br>
solving infinite sums. Usually PME is a poor choice for in vacuo<br>
simulations and the like, since there's nothing to be done for most of<br>
the simulation box.<br>
</blockquote>
<br></div>
This interests me -I've used simple cut-off for in vacuo tests, but I still hadn't made my mind on what electrostatic model I should truly use. Do you have any suggestion?<br>
<br>
thanks,<br><font color="#888888">
M.</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
You may want to see how others (in the literature)<br>
deal with droplet-type simulations.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Thanks for your help.<br>
<br>
Sapna<br>
<br>
On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<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>
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<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>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<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. --<br>
George Bernard Shaw.<br>
Dare to Dream<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
-- <br></div></div><div><div></div><div class="h5">
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</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>