<br><br><div class="gmail_quote">On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian <span dir="ltr"><<a href="mailto:xianshine@gmail.com">xianshine@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="ZH-CN" link="blue" vlink="purple"><div><p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I have sent this email days ago, but I got no answer.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Hope someone would saw it this time. <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Sorry for disturbing.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US">Dear all:<u></u><u></u></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.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> I have a question.<u></u><u></u></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:<u></u><u></u></span></p>
<p style="margin-left:39.0pt"><u></u><span lang="EN-US"><span>1.<span style="font:7.0pt "Times New Roman""> </span></span></span><u></u><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>
</div></div></blockquote><div>Yes, you have to switch to cutoff for coulomb interaction. I have seen in other publications that they use a regular coulomb with cutoff as large as 2 nm. I am not sure whether there is any advantage in using Reaction field.</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="ZH-CN" link="blue" vlink="purple"><div><p style="margin-left:39.0pt"><span lang="EN-US"><u></u><u></u></span></p>
<p style="margin-left:39.0pt"><u></u><span lang="EN-US"><span>2.<span style="font:7.0pt "Times New Roman""> </span></span></span><u></u><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>
</div></div></blockquote><div> I have had no problems in using LINCS during local pressure calculation.</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="ZH-CN" link="blue" vlink="purple">
<div><p style="margin-left:39.0pt"><span lang="EN-US"> <u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal" style="margin-left:21.0pt"><span lang="EN-US">Thanks for any reply.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:21.0pt"><span lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal" style="margin-left:21.0pt"><span lang="EN-US">Best wishes, <u></u><u></u></span></p><p class="MsoNormal" style="margin-left:21.0pt">
<span lang="EN-US">KONG Xian<u></u><u></u></span></p><p class="MsoNormal" style="margin-left:21.0pt"><span lang="EN-US">Tsinghua, Beijing, China<u></u><u></u></span></p><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><u></u><u></u></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 href="http://www.eset.com" target="_blank">http://www.eset.com</a><br> </div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>