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--></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><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: chrishengbee@hust.edu.cn<br>Phone: (86)27-87548122 <br>http://itp.energy.hust.edu.cn </p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div 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 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 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 lang=ZH-CN style='font-family:DengXian'>。</span></p><p class=MsoNormal> Best regards<span lang=ZH-CN style='font-family:DengXian'>！</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: chrishengbee@hust.edu.cn<br>Phone: (86)27-87548122 <br>http://itp.energy.hust.edu.cn </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></div></body></html>