<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Apr 16, 2010, at 1:40 AM, Shuangxing Dai wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">I am not running in parallel. Right now I just changed links order from 12 to 4. It is still slow. While I change to shift, not Ewald, it finished 10000 steps in 10 mins. In the paper: <div><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 12px; line-height: 18px; "><div style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; font-size: 0.91666em; line-height: 1.45em; ">
<a href="javascript:AL_get(this,%20'jour',%20'J%20Comput%20Chem.');" title="Journal of computational chemistry." style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">J Comput Chem.</a> 2005 Dec;26(16):1701-18.</div>
<h1 class="title" style="font-size: 1.3333em; line-height: 1.125em; font-weight: bold; margin-top: 0.375em; margin-right: 0px; margin-bottom: 0.375em; margin-left: 0px; "><a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.103.418&rep=rep1&type=pdf">GROMACS: fast, flexible, and free.</a></h1><div style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; "><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Van%20Der%20Spoel%20D%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Van Der Spoel D</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lindahl%20E%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Lindahl E</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Hess%20B%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Hess B</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Groenhof%20G%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Groenhof G</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Mark%20AE%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Mark AE</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Berendsen%20HJ%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Berendsen HJ</a>.</div><div style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; "> The performance there is around 10000 ps/day. I do not understand why my speed is so slow and it seems</div></span></div></div></blockquote><blockquote type="cite"><div dir="ltr"><div><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 12px; line-height: 18px; "><div style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; ">that Ewald option makes it slow. </div></span></div></div></blockquote>Hi,</div><div><br></div><div>why don't you use PME then? It can also be used in parallel.</div><div>Ewald is not optimized for speed.</div><div><br></div><div>Carsten</div><div><br></div><div><br></div></body></html>