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Hi,<br>No warning was found. Is it because the use of "User" vdw potential?<br>The mdp file is the following:<br><br>title = A<br>cpp = cpp<br>include = -I../top<br>define =<br>integrator = md<br>dt = 0.001<br>nsteps = 10000<br>nstxout = 1000<br>nstvout = 1000<br>nstlog = 1000<br>nstenergy = 1000<br>nstxtcout = 0<br>energygrps = CGW CBB HAL NBB OBB<br>coulombtype = User<br>rcoulomb = 1.1<br>nstlist = -1<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.1<br>vdwtype = User<br>rvdw = 1.1<br>table-extension = 0.<br>energygrp_table = CGW CGW CGW HAL CGW NBB CGW OBB CGW CBB CBB CBB CBB NBB CBB OBB CBB HAL HAL HAL HAL NBB HAL OBB NBB NBB NBB OBB OBB OBB<br>tcoupl = nose-hoover<br>tc_grps = System<br>tau_t = 0.1<br>ref_t = 310<br>pcoupl = no<br>gen_vel = yes<br>gen_temp = 310<br>gen_seed = 173529<br><br>Thanks.<br>Lanyuan<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] "nstlist=-1" and performance problem<br>Date: Wed, 28 Jan 2009 23:22:30 +0100<br><br>
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Hi,<br><br>But grompp should have given a warning about this.<br>You should have only obtained a tpr file when using the -maxwarn option of grompp.<br>Or did grompp not give a warning about the buffer being too small?<br><br>Berk<br><br><hr id="EC_stopSpelling">From: lulanyuan@msn.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] "nstlist=-1" and performance problem<br>Date: Wed, 28 Jan 2009 17:12:00 -0500<br><br>
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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_EC_stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] "nstlist=-1" and performance problem<br>Date: Wed, 28 Jan 2009 10:42:59 +0100<br><br>
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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_EC_stopSpelling">From: lulanyuan@msn.com<br>To: gmx-users@gromacs.org<br>Date: Mon, 26 Jan 2009 17:31:43 -0500<br>Subject: [gmx-users] "nstlist=-1" and performance problem<br><br>
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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. <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！ <a href="http://im.live.cn/imme/">现在就下载！</a><br><hr>Express yourself instantly with MSN Messenger! <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！ <a href="http://im.live.cn/newsexpress">了解详细！</a><br><hr>See all the ways you can stay connected <a href="http://www.microsoft.com/windows/windowslive/default.aspx">to friends and family</a><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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