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</o:shapelayout></xml><![endif]--></head><body lang=ZH-CN link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for your important advice, I am extending my simulation to 60ns, if it is still not long enough, I’ll extend another time. Thank you.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal align=left style='text-align:left'><b><span style='font-size:10.0pt;font-family:宋体'>发件人<span lang=EN-US>:</span></span></b><span lang=EN-US style='font-size:10.0pt;font-family:宋体'> Jianguo Li [mailto:ljggmx@yahoo.com.sg] <br></span><b><span style='font-size:10.0pt;font-family:宋体'>发送时间<span lang=EN-US>:</span></span></b><span lang=EN-US style='font-size:10.0pt;font-family:宋体'> 2011</span><span style='font-size:10.0pt;font-family:宋体'>年<span lang=EN-US>8</span>月<span lang=EN-US>22</span>日<span lang=EN-US> 9:52<br></span><b>收件人<span lang=EN-US>:</span></b><span lang=EN-US> KONG Xian<br></span><b>主题<span lang=EN-US>:</span></b><span lang=EN-US> Re: Re</span>：<span lang=EN-US>the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure<o:p></o:p></span></span></p></div></div><p class=MsoNormal align=left style='text-align:left'><span lang=EN-US><o:p> </o:p></span></p><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><div><div><div><p class=MsoPlainText><span lang=EN-US>Thanks for your kindly reply. <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>I used the LINCS calculated the pressure field. The distinct between protein and the lipid bilayer is obvious from the pressure field. <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>But the lipid bilayer and the water is not very obvious , they seems to be a uniform from the pressure field calculated. As in Ollila</span><span lang=EN-US style='font-family:"Courier New"'>’</span><span lang=EN-US>s original paper: <i>3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes,</i> there is an distinct separation region between membrane and the water.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Maybe the LINCS is the problem.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Another problem is perhaps the localpressure software is for CG model? My model is all-atom model and the simulation time length is not long enough, maybe this is the cause of the results?<o:p></o:p></span></p><p class=MsoPlainText style='margin-bottom:12.0pt'><span lang=EN-US>From my limited experience, the local pressure calculation converges very poorly. It takes more than 50 ns of production run in my case to get a converged profile. You can divide the production run into several sub-trajectories to judge the convergence.<br><br><o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>KONG Xian<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>2011/8/21<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Hi, Kong Xian,<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 9, 3882b3893.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>best regards,<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Jianguo <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>________________________________<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>From: KONG Xian <<a href="mailto:xianshine@gmail.com" target="_blank">xianshine@gmail.com</a>><o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Sent: Friday, 19 August 2011 23:50:01<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Subject: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>I have sent this email days ago, but I got no answer.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Hope someone would saw it this time. <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Sorry for disturbing.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Dear all:<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> I have a question.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions:<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>1. I changed the The coulomb interaction type from PME to reaction field <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>with epsilon_r=1 epsilon_rf=78; Is this change feasible?<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>2. I used LINCS for all bonds in the simulation, and I still use the LINCS <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>for all bonds when calculate the local pressure. Is this way right? <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US> <o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Thanks for any reply.<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Best wishes,<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>KONG Xian<o:p></o:p></span></p><p class=MsoPlainText><span lang=EN-US>Tsinghua, Beijing, China<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div><p class=MsoNormal align=left style='text-align:left'><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br><br>__________ Information from ESET NOD32 Antivirus, version of virus signature database 6397 (20110821) __________<br><br>The message was checked by ESET NOD32 Antivirus.<br><br><a href="http://www.eset.com" target="_blank">http://www.eset.com</a><br><br><o:p></o:p></span></p></div></div></div><p class=MsoNormal align=left style='text-align:left'><span lang=EN-US style='font-size:12.0pt;font-family:宋体'><br><br>__________ Information from ESET NOD32 Antivirus, version of virus signature database 6398 (20110821) __________<br><br>The message was checked by ESET NOD32 Antivirus.<br><br><a href="http://www.eset.com">http://www.eset.com</a><o:p></o:p></span></p></div> <BR><BR>__________ Information from ESET NOD32 Antivirus, version of virus signature database 6402 (20110823) __________<BR><BR>The message was checked by ESET NOD32 Antivirus.<BR><BR><A HREF="http://www.eset.com">http://www.eset.com</A><BR> </body></html>