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<div class="moz-cite-prefix">Hi,<br>
<br>
You are right. I filed a redmine issue:<br>
<a class="moz-txt-link-freetext" href="http://redmine.gromacs.org/issues/1916">http://redmine.gromacs.org/issues/1916</a><br>
And I uploaded a fix for the release-5-0 branch:<br>
<a class="moz-txt-link-freetext" href="https://gerrit.gromacs.org/#/c/5701/">https://gerrit.gromacs.org/#/c/5701/</a><br>
<br>
Thanks for reporting this.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/08/2016 04:11 AM, Sheng Bi wrote:<br>
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<p class="MsoNormal">Here we find gromacs goes wrong when using
verlet and 3dc an run in parallel.</p>
<p class="MsoNormal">For slab geometry, we need to do slab
correction based on total charge dipole ( mu_tot=sum(qi*zi) ).
If one performs such simulation in gromacs with Verlet and 3dc
in parallel (especially using domain decomposition), the
mu_tot is wrong. For example, if you run simulation in 16
core, and the right global charge dipole is A, however in gmx
4.6 and higher each core would get 16*A!</p>
<p class="MsoNormal">I think the problem come out on this
communication, for version 4.6, gmx sum charge dipole twice.
In sim_util.c, line 1052:</p>
<p class="MsoNormal"> /* When we don't need the total
dipole we sum it in global_stat */</p>
<p class="MsoNormal"> if (bStateChanged &&
NEED_MUTOT(*inputrec))</p>
<p class="MsoNormal"> {</p>
<p class="MsoNormal"> gmx_sumd(2*DIM, mu, cr);</p>
<p class="MsoNormal"> }</p>
<p class="MsoNormal">if using domain decomposition, gmx will sum
the dipole for the first time. However in line 1090:</p>
<p class="MsoNormal"> if (bStateChanged &&
NEED_MUTOT(*inputrec))</p>
<p class="MsoNormal"> {</p>
<p class="MsoNormal"> if (PAR(cr))</p>
<p class="MsoNormal"> {</p>
<p class="MsoNormal"> gmx_sumd(2*DIM, mu, cr);</p>
<p class="MsoNormal"> }</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> for (i = 0; i < 2; i++)</p>
<p class="MsoNormal"> {</p>
<p class="MsoNormal"> for (j = 0; j < DIM; j++)</p>
<p class="MsoNormal"> {</p>
<p class="MsoNormal"> fr->mu_tot[i][j] =
mu[i*DIM + j];</p>
<p class="MsoNormal"> }</p>
<p class="MsoNormal"> }</p>
<p class="MsoNormal"> }</p>
<p class="MsoNormal">gmx sum the dipole for second time only if
run in parallel. So, if you perform simulation in 3dc with
verlet and in domain decomposition, the mu_tot will go wrong.</p>
<p class="MsoNormal">Since we performed a lot of slab geometry
simulatin and gmx worked perfect in version 3.3 and 4.5, when
we use 4.6 and higher, we find this problem. Is this a bug or
my setup error in mdp<span style="font-family:DengXian"
lang="ZH-CN">？</span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">--<br>
PhD student<br>
State Key Laboratory of Coal Combustion,<br>
School of Energy and Power Engineering,<br>
Huazhong University of Science and Technology (HUST),<br>
Room 302 Power Building, <br>
1037 Luoyu Road, Wuhan, Hubei 430074 China<br>
Email: <a class="moz-txt-link-abbreviated" href="mailto:chrishengbee@hust.edu.cn">chrishengbee@hust.edu.cn</a><br>
Phone: (86)27-87548122 <br>
<a class="moz-txt-link-freetext" href="http://itp.energy.hust.edu.cn">http://itp.energy.hust.edu.cn</a> </p>
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<p class="MsoNormal"><o:p> </o:p></p>
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