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Hi,<br>It's in the gmx4.0 manual. Just check the part for mdp options. I guess it is the method in DLPOLY and many text books.<br>Lanyuan<br><br><hr id="stopSpelling">From: x.periole@rug.nl<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] "nstlist=-1" and performance problem<br>Date: Wed, 28 Jan 2009 23:28:25 +0100<br><br>Hi,<div><br></div><div>Any documentation on how this is actually done? </div><div><br></div><div>Sounds interesting!</div><div><br></div><div>XAvier.</div><div><br><div><div>On Jan 28, 2009, at 11:12 PM, LuLanyuan wrote:</div><br class="EC_Apple-interchange-newline"><blockquote><span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div class="EC_hmmessage" style="font-size: 10pt; font-family: Verdana;">Hi Berk,<br>Thanks very much. I've found the problem. As you said I forgot to increase rvdw. So the buffer is zero and the system needs to update the nblist every step, which is obviously wrong. After I corrected the mistake, the speed for "nstlist=-1" is roughly three times faster as I expected.<br>Lanyuan<br><br><hr id="EC_stopSpelling">From:<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a><br>To:<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: RE: [gmx-users] "nstlist=-1" and performance problem<br>Date: Wed, 28 Jan 2009 10:42:59 +0100<br><br>Hi,<br><br>I assume you did not only change nstlist, but also other mdp settings, or not?<br><br>Changing only nstlist from 1 to -1 should result in nearly equal or much faster speeds.<br><br>For efficient simulations with nslist=-1 you need to set an appropriate<br>buffer region (rlist > rcoulomb=rvdw). In 4.0 you have to optimize this by hand.<br>It would be nice to have this automated.<br>At the end of the log file (a run of a few minutes is enough) you can see what<br>the neighborlist lifetime is. Optimal is usually something between 10 and 20.<br>Play with rlist to optimize the performance (also printed at the end of the log file).<br><br>Berk<br><br><hr id="EC_EC_stopSpelling">From:<span class="EC_Apple-converted-space"> </span><a href="mailto:lulanyuan@msn.com">lulanyuan@msn.com</a><br>To:<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Date: Mon, 26 Jan 2009 17:31:43 -0500<br>Subject: [gmx-users] "nstlist=-1" and performance problem<br><br>Hello,<br>Could Berk or someone else answer my question regarding the new "nstlist=-1" option in gmx4? In my understanding, the algorithm for this option is the one used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with "nstlist=-1" and "nstlist=1", I found the speeds were basically the same. Isn't this automatic nblist checking supposed to be faster than updating the nblist every step? I also did similar tests on LAMMPS for the same system and found the speed for automatical updating was several times faster. As a result, although Gromacs is about 60% faster if we choose nstlist=1, it's much slower than LAMMPS if we choose the automatic nblist updating.<span class="EC_Apple-converted-space"> </span><br>Thanks in advance for any ideas about it.<br>Lanyuan Lu<br><br><br><hr>不加好友也能聊？试试MSN在线通！<span class="EC_Apple-converted-space"> </span><a href="http://im.live.cn/imme/">现在就下载！</a><br><hr>Express yourself instantly with MSN Messenger!<span class="EC_Apple-converted-space"> </span><a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a><br><hr>八卦娱乐包打听，MSN资讯速递帮你忙！<span class="EC_Apple-converted-space"> </span><a href="http://im.live.cn/newsexpress">了解详细！</a><span class="EC_Apple-converted-space"> </span>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="EC_Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="EC_Apple-converted-space"> </span><br>www interface or send it to<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div><br /><hr />更多热辣资讯尽在新版MSN首页！ <a href='http://cn.msn.com/' target='_new'>立刻访问！</a></body>
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