<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">Dear all,</SPAN></FONT></P><P class="MsoNormal"></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">I wonder if GROMACS can do simulations on restrainted set of structures, in order to simulate ensemble of structures as described by Dr Vendruscolo (e.g. Vendruscolo, M., Paci, E., Dobson, C.M. & Karplus, M. Three key residues form a critical contact network in a transition state for protein folding. Nature 409, 641−645 (2001).).</SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;"><BR class="khtml-block-placeholder"></SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">If yes, how to do this? Can it be done using –multi?</SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;"> </SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">And if not, how can it be implemented in GROMACS? </SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;"> </SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">Thanks, Itamar.</SPAN></FONT></P><DIV><DIV></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">===========================================</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Itamar Kass</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| The Alexander Silberman</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Institute of Life Sciences</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Department of Biological Chemistry</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| The Hebrew University, Givat-Ram</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Jerusalem, 91904, Israel</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Tel: +972-(0)2-6585194</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Fax: +972-(0)2-6584329</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Email: <A href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</A></SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">| Homepage: <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></SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;">============================================</SPAN></FONT></DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;"><BR class="Apple-interchange-newline"></SPAN></FONT></DIV><FONT class="Apple-style-span" color="#00000000"><SPAN class="Apple-style-span" style="background-color: transparent;"><BR></SPAN></FONT></BODY></HTML>