<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi, Kong Xian,<br><br>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<br>bilayers from molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 9, 3882–3893.<br><br>best regards,<br>Jianguo <br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> KONG Xian <xianshine@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight:
bold;">Sent:</span></b> Friday, 19 August 2011 23:50:01<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure<br></font><br><meta http-equiv="x-dns-prefetch-control" content="off">
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--></style><div class="WordSection1"><p class="MsoNormal"><span style="color:#1F497D;" lang="EN-US">I have sent this email days ago, but I got no answer.</span></p><p class="MsoNormal"><span style="color:#1F497D;" lang="EN-US">Hope someone would saw it this time. </span></p><p class="MsoNormal"><span style="color:#1F497D;" lang="EN-US">Sorry for disturbing.</span></p><p class="MsoNormal"><span lang="EN-US">Dear all:</span></p><p class="MsoNormal"><span lang="EN-US"> I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system.</span></p><p class="MsoNormal"><span lang="EN-US"> I have a question.</span></p><p class="MsoNormal"><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:</span></p><p class="MsoListParagraph" style="margin-left:39.0pt;"><span lang="EN-US"><span style="">1.<span style="font:7.0pt "Times New Roman";"> </span></span></span><span lang="EN-US">I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible?</span></p><p class="MsoListParagraph" style="margin-left:39.0pt;"><span lang="EN-US"><span style="">2.<span style="font:7.0pt "Times New Roman";"> </span></span></span><span lang="EN-US">I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? </span></p><p class="MsoNormal"><span lang="EN-US"> </span></p><p class="MsoNormal" style="margin-left:21.0pt;"><span lang="EN-US">Thanks for any reply.</span></p><p class="MsoNormal"
style="margin-left:21.0pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="margin-left:21.0pt;"><span lang="EN-US">Best wishes, </span></p><p class="MsoNormal" style="margin-left:21.0pt;"><span lang="EN-US">KONG Xian</span></p><p class="MsoNormal" style="margin-left:21.0pt;"><span lang="EN-US">Tsinghua, Beijing, China</span></p><p class="MsoNormal" style="text-align:left;" align="left"><span style="font-size:12.0pt;font-family:"serif";" lang="EN-US"><br><br></span></p></div> <br><br>__________ Information from ESET NOD32 Antivirus, version of virus signature database 6393 (20110819) __________<br><br>The message was checked by ESET NOD32 Antivirus.<br><br><a rel="nofollow" target="_blank" href="http://www.eset.com">http://www.eset.com</a><br> <meta http-equiv="x-dns-prefetch-control" content="on"></div></div>
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