<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><SPAN class="Apple-style-span"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Comic Sans MS"><FONT class="Apple-style-span" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">Shalom Rob,</SPAN></FONT></FONT></FONT></SPAN><DIV><SPAN class="Apple-style-span"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Comic Sans MS"><FONT class="Apple-style-span" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"> Try to look at the gromacs site (<A href="http://www.gromacs.org/contributions/index.php">http://www.gromacs.org/contributions/index.php</A>) look for a file named </SPAN></FONT></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Comic Sans MS"><FONT class="Apple-style-span" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">mdrun_make_hole.tar.gz which is used as a modifier of gromacs 3.1.4. This enable GROMACS to make a hole in a membrane based on the inserted protein surface (you also need msms).</SPAN></FONT></FONT></FONT></SPAN><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Comic Sans MS"><FONT class="Apple-style-span" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"> The protocol is based on </SPAN></FONT></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Comic Sans MS"><FONT class="Apple-style-span" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">Faraldo-Gomez, J<FONT class="Apple-style-span" color="#000000">. D., Smith, G. R., and Sansom, M. S. (2002). Setting up and optimization of membrane protein simulations. </FONT><FONT class="Apple-style-span" color="#000000">European Biophysics Journal 31(3), 217-227.</FONT></SPAN></FONT></FONT></FONT></DIV><DIV><DIV><FONT class="Apple-style-span" face="Comic Sans MS"><FONT class="Apple-style-span" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"> Itamar.</SPAN></FONT></FONT></DIV><DIV><SPAN class="Apple-style-span"><FONT class="Apple-style-span" color="#002DFA" face="Times" size="4"><SPAN class="Apple-style-span" style="font-size: 16px;"><FONT class="Apple-style-span" color="#000000" face="Comic Sans MS" size="6"><SPAN class="Apple-style-span" style="font-size: 20px;"><BR></SPAN></FONT></SPAN></FONT><DIV><DIV>On Jun 27, 2005, at 7:08 PM, rob yang wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">hi,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">i am trying to simulate glycophorin A dimeric helix in explicit lipid bilayer membrane environment (say, POPC or DMPC). i know that the charmm people have a standard protocol to set up md using CHARMM. i am just wondering if the gromacs community has a standard protocol for such simulations. i've tried to followed the tutorial provided by richard law (<A href="http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm">http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm</A>) but would like to have a more systematic way of setting up the membrane and positioning the helix dimer.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">i also tried the gramicidin A tutorial (<A href="http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/">http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/</A>) which was very helpful.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">however, the lipid building step did not seem to use a pre-equilibrated lipid library. could anybody give me a pointer to a more elaborated protocol in setting up and running this type of simulation using gromacs? thank you very much in advance.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV> <BR class="Apple-interchange-newline"></BLOCKQUOTE></DIV><BR><DIV> <DIV><BR class="khtml-block-placeholder"></DIV><BR><DIV><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">===========================================</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Itamar Kass</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| The Alexander Silberman</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Institute of Life Sciences</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Department of Biological Chemistry</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| The Hebrew University, Givat-Ram</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Jerusalem, 91904, Israel</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Tel: +972-(0)2-6585146</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Fax: +972-(0)2-6584329</P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Email: <A href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</A></P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">| Net: <A href="http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html">http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html</A></P><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica">============================================</P></DIV> </DIV><BR></SPAN></DIV></DIV></DIV></BODY></HTML>