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<div class="moz-cite-prefix">Hi,<br>
<br>
I think you misinterpreted the code in ewald_LRcorrection. It does
the same things in 3.3.1 and 4.6.7.<br>
My guess is that the issue you are observing is due to periodic
boundary conditions. With group cut-off scheme charge groups are
whole (not split by PBC), so water molecules are usually whole.
Then the 3DC correction always works correctly when you have
charge groups with zero net charge. In the Verlet cut-off scheme
with domain decomposition, or with charged charge groups,
(partial) charges moving over PBC change the system dipole. To get
your system to run correctly you need to ensure that no water
molecule moves over the periodic boundary in along the
z-dimension. I think grompp will print a warning for this issue.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-06-07 10:12, Sheng Bi wrote:<br>
</div>
<blockquote cite="mid:5756863B.019A35.28023@mail.hust.edu.cn"
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<p class="MsoNormal">Sorry, some type-offs in previous question.</p>
<p class="MsoNormal">In gmx-4.6.7, ewald_LRcorrection()<b>.</b>
We loop over excluded neighbours only in condition <b>calc_excl_corr=1</b>.
But when using Verlet cut-off scheme, <b>calc_excl_corr will
be 0</b>.</p>
<p class="MsoNormal"><o:p> </o:p></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>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><o:p> </o:p></span></p>
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style="mso-element:para-border-div;border:none;border-top:solid
#E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="border:none;padding:0in"><b>From:
</b><a moz-do-not-send="true"
href="mailto:chrishengbee@hust.edu.cn">Sheng Bi</a><br>
<b>Sent: </b>Tuesday, June 7, 2016 1:28 AM<br>
<b>To: </b><a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<b>Subject: </b>[gmx-developers] Question about
ewald_LRcorrection() function</p>
</div>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal">Dear GMX developers:</p>
<p class="MsoNormal"> I find a abnormal phenomenon
when using <b>gromacs-4.6.7</b>. I set up a system containing
two walls(consist of freeze atoms), one wall has positively
charges on atoms, another has negatively charges. I put an
water molecule(rigid spc/spce/tip3p model) between these two
walls. <b>Whole system seems like below</b>:</p>
<p class="MsoNormal">
****************************************</p>
<p class="MsoNormal"> * -
H
+ * </p>
<p class="MsoNormal"> * - \
+
vacuum *</p>
<p class="MsoNormal"> * -
O
+ *</p>
<p class="MsoNormal"> * -
/
+ *</p>
<p class="MsoNormal"> * - H
+ *</p>
<p class="MsoNormal">
****************************************</p>
<p class="MsoNormal"> I use <b>Verlet cut-off
scheme, PME method, and ewald-geometry=3DC</b>. Temperature
of whole system is at <b>0K</b>, controlled by <b>v-rescale
method</b>. I run whole simulation <b>only in OPENMP
parallel</b>.</p>
<p class="MsoNormal"> One can have following
expected behavior of water molecule without MD simulation:
Since it can be seen as an infinite panel capacitor, <b>there
is constant electric field between two walls. So the water
will change it orientation, but won’t change it’s
position(Since 0K)</b>.</p>
<p class="MsoNormal"> This phenomenon can be <b>confirmed
by gromcas-3.3.1</b> (although there is position shift, but
quite small). Also, if one use higher version of gromacs, such
as 4.6.7 or higher <b>with ewald-geometry=3D, either no
problem</b>. However, if one use <b>3DC</b> (and it should
be), you can see <b>an obvious force on water molecule</b>.</p>
<p class="MsoNormal"> I hacked into source code,
and find this might due to <b>ewald_LRcorrection()</b>
function:</p>
<p class="MsoNormal"> Firstly, in gmx-4.6.7,
ewald_LRcorrection()<b>.</b> We <b>loop over excluded
neighbours only in condition calc_excl_corr=0. But when
using verlet cut-off scheme, calc_excl_corr will be 1</b>.
In gmx-3.3.1, we do loop over excluded neighbours without
additional if() statement.</p>
<p class="MsoNormal"> Secondly, in gmx-4.6.7, ,
ewald_LRcorrection(). When do dipole correction on force, we
loop over <b>excl_load</b> (Exclusion load distribution over
the threads). In fact, most water model will have nrexel=2.
So, as a result, we <b>only do dipole correction on O atom,
but do nothing on H atoms</b> and we will see an obvious
force on the whole water molecule. I think this is not purpose
of 3DC<span style="font-family:DengXian" lang="ZH-CN">。</span></p>
<p class="MsoNormal"> Best regards<span
style="font-family:DengXian" lang="ZH-CN">!</span></p>
<p class="MsoNormal">Sheng Bi</p>
<p class="MsoNormal"><b> </b></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>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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