Thank you very much. I thought gromacs should do that but also a very useful suggestion for checking that.<br><br>-Swarnendu<br><br><div class="gmail_quote">On Mon, Mar 14, 2011 at 9:54 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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"><br><br><span>On 15/03/11, <b>Swarnendu Tripathi </b> <<a href="mailto:stripat1@kent.edu" target="_blank">stripat1@kent.edu</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>Hello everyone,<br><br>In gromacs when the Coulomb interactions are calculated are they calculated for the all atom pairs or only for the charged atoms pairs? </div></blockquote><br></div>GROMACS notices atoms with zero charge and does not put them into lists scheduled for evaluating charge-charge interactions. Similarly for zero LJ parameters.<div class="im">
<br><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div>If the Coulomb interactions are not calculated only for the charged atoms then how can I modify the gromacs to do that. In my system I have only 27 charged atoms and I want gromacs to calculate the Coulomb interactions only for these atoms. I am using gromacs 4.0.7.</div>
</blockquote><br></div>Obviously, this is only an efficiency issue, and GROMACS already takes care of it. You could see that this is true by making all of your "uncharged" atoms have charge 0.000001 and observing the increase in run time. You can also see this from the breakdown of computation time at the end of your .log file. There will be significant time spent doing LJ-only loops, and less time doing LJ+Coulomb loops.<br>
<font color="#888888"><br>Mark<br><div><br>
</div>
</font><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>