<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">You might want to try Simbody (simtk.org). This will allow you to rigidify any part or parts of the molecule you choose. As a bonus, you will not spend resources computing intramolecular interactions in the rigidified regions. <div><br></div><div>Sam</div><div><br><div><html>On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote:</html><br class="Apple-interchange-newline"><blockquote type="cite"><br><br>vivek sharma wrote:<br><blockquote type="cite">Hi justin,<br></blockquote><blockquote type="cite">My apologies for asking you so many small queries.<br></blockquote><blockquote type="cite">Can you suggest any good tutorial or reference that talks about this issue of running MD over a selected part of molecule.<br></blockquote><br>If you're using PR, all you're doing is position-restrained dynamics.<br><br>-Justin<br><br><blockquote type="cite">With Thanks,<br></blockquote><blockquote type="cite">Vivek<br></blockquote><blockquote type="cite">2008/10/10 vivek sharma <viveksharma.iitb@gmail.com <<a href="mailto:viveksharma.iitb@gmail.com">mailto:viveksharma.iitb@gmail.com</a>>><br></blockquote><blockquote type="cite"> hI justin,<br></blockquote><blockquote type="cite"> Thanks for your response.<br></blockquote><blockquote type="cite"> do I need to specify the index file(for residue that I want to keep<br></blockquote><blockquote type="cite"> fix during MD) during GROMPP or just including the psre.itp in<br></blockquote><blockquote type="cite"> topology is enough for the purpose ?<br></blockquote><blockquote type="cite"> With Thanks,<br></blockquote><blockquote type="cite"> Vivek<br></blockquote><blockquote type="cite"> 2008/10/10 Justin A. Lemkul <jalemkul@vt.edu <<a href="mailto:jalemkul@vt.edu">mailto:jalemkul@vt.edu</a>>><br></blockquote><blockquote type="cite"> Justin A. Lemkul wrote:<br></blockquote><blockquote type="cite"> vivek sharma wrote:<br></blockquote><blockquote type="cite"> Thanks Justin,<br></blockquote><blockquote type="cite"> My goal is to keep certain part fixed and move only a<br></blockquote><blockquote type="cite"> few of the residues (case is like providing flexibility<br></blockquote><blockquote type="cite"> to the site of interest only).<br></blockquote><blockquote type="cite"> SO , do I need to specify the residue using some index<br></blockquote><blockquote type="cite"> file ?<br></blockquote><blockquote type="cite"> or is there some other way to specify the part of<br></blockquote><blockquote type="cite"> molecule for position restraining ??<br></blockquote><blockquote type="cite"> Make an index file with the residues you want to keep fixed, and<br></blockquote><blockquote type="cite"> pass it<br></blockquote><blockquote type="cite"> to genpr to generate a new posre.itp that corresponds to those<br></blockquote><blockquote type="cite"> residues.<br></blockquote><blockquote type="cite"> -Justin<br></blockquote><blockquote type="cite"> With Thanks,<br></blockquote><blockquote type="cite"> Vivek<br></blockquote><blockquote type="cite"> 2008/10/10 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br></blockquote><blockquote type="cite"> <<a href="mailto:jalemkul@vt.edu">mailto:jalemkul@vt.edu</a>> <<a href="mailto:jalemkul@vt.edu">mailto:jalemkul@vt.edu</a><br></blockquote><blockquote type="cite"> <<a href="mailto:jalemkul@vt.edu">mailto:jalemkul@vt.edu</a>>>><br></blockquote><blockquote type="cite"> vivek sharma wrote:<br></blockquote><blockquote type="cite"> Hi there,<br></blockquote><blockquote type="cite"> I want to run MD over a part of my molecule ,<br></blockquote><blockquote type="cite"> for few residues<br></blockquote><blockquote type="cite"> only (not the whole molecule).<br></blockquote><blockquote type="cite"> Can I do it using GROMACS ?<br></blockquote><blockquote type="cite"> I searched for the online documentation and<br></blockquote><blockquote type="cite"> mailing list, but<br></blockquote><blockquote type="cite"> unable to get appropriate information.<br></blockquote><blockquote type="cite"> If somebody has already tried such things<br></blockquote><blockquote type="cite"> earlier, please<br></blockquote><blockquote type="cite"> suggest and direct me for appropriate link and<br></blockquote><blockquote type="cite"> address.<br></blockquote><blockquote type="cite"> Well, if your goal is to keep certain parts fixed and<br></blockquote><blockquote type="cite"> allow others<br></blockquote><blockquote type="cite"> to move, probably the easiest way to do it is to<br></blockquote><blockquote type="cite"> apply position<br></blockquote><blockquote type="cite"> restraints to the "fixed" part.<br></blockquote><blockquote type="cite"> -Justin<br></blockquote><blockquote type="cite"> With Thanks,<br></blockquote><blockquote type="cite"> Vivek<br></blockquote><blockquote type="cite"> ------------------------------------------------------------------------<br></blockquote><blockquote type="cite"> _______________________________________________<br></blockquote><blockquote type="cite"> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"> <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>><br></blockquote><blockquote type="cite"> <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"> <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>>><br></blockquote><blockquote type="cite"> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite"> Please search the archive at<br></blockquote><blockquote type="cite"> <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><br></blockquote><blockquote type="cite"> before posting!<br></blockquote><blockquote type="cite"> Please don't post (un)subscribe requests to the<br></blockquote><blockquote type="cite"> list. 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line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Samuel Coulbourn Flores, PhD</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Altman Lab</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Department of BioEngineering</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Stanford University</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; "><a href="mailto:samuel.flores@aya.yale.edu">samuel.flores@aya.yale.edu</a></span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">650.644.8416</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; "><br class="webkit-block-placeholder"></span></font></div><div><span class="Apple-style-span" style="font-family: 'Hiragino Maru Gothic Pro'; font-size: 15px; white-space: pre-wrap; ">花山</span></div><div><span class="Apple-style-span" style="font-family: 'Hiragino Maru Gothic Pro'; font-size: 15px; white-space: pre-wrap; ">科学者</span></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">生物工学部</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">スタンフォ一ド大学</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">スタンフォ一ド、<span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; white-space: normal; "><span class="Apple-style-span" style="font-family: 'Hiragino Maru Gothic Pro'; font-size: 15px; white-space: pre-wrap; ">カリフォルニア、米国</span></span></span></font></div><div><br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder"></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>