<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; 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 bgcolor="#ffffff"><div><font face="MS UI Gothic" size="2">I tried Martini force field and found it calculates with a good result in appearance</font></div><div><font face="MS UI Gothic" size="2">for a *specific* c</font><font face="MS UI Gothic" size="2">alculation prepared at the Martini website.</font></div></div></span></blockquote><span class="Apple-style-span" style="font-size: small;">T</span><span class="Apple-style-span" style="font-size: small;">h</span><span class="Apple-style-span" style="font-size: small;">a</span><span class="Apple-style-span" style="font-size: small;">t</span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-size: small;">i</span><span class="Apple-style-span" style="font-size: small;">s</span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-size: small;">g</span><span class="Apple-style-span" style="font-size: small;">o</span><span class="Apple-style-span" style="font-size: small;">o</span><span class="Apple-style-span" style="font-size: small;">d</span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-size: small;">t</span><span class="Apple-style-span" style="font-size: small;">o</span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-size: small;">k</span><span class="Apple-style-span" style="font-size: small;">n</span><span class="Apple-style-span" style="font-size: small;">o</span><span class="Apple-style-span" style="font-size: small;">w</span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-size: small;">:</span><span class="Apple-style-span" style="font-size: small;">)</span><span class="Apple-style-span" style="font-size: small;">)</span><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; 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 bgcolor="#ffffff"><div><font face="MS UI Gothic" size="2">Now, I wish to use another small molecule (such as lipid) for CG simulation.</font></div><div><font face="MS UI Gothic" size="2">Starting from the chemical structure, I draw it with<span class="Apple-converted-space"> </span></font><font face="MS UI Gothic" size="2">MarvinSketch</font></div><div><font face="MS UI Gothic" size="2">and save as pdb. After this I want to make a .gro file and .itp file</font></div><div><font face="MS UI Gothic" size="2">which is compatible for Martini force field. Can u give me instruction</font></div><div><font face="MS UI Gothic" size="2">for that? </font></div></div></span></blockquote>you can find the main steps to build your own "martini" molecule in</div><div>a couple of papers. This is decribed in detail for lipids and amino-acid </div><div>in most recent papers:</div><div>Marrink et al J. Phys. Chem. B, 2007, 111 (27), pp 7812–7824</div><div>Montecelli et al J. Chem. Theory Comput., 2008, 4 (5), pp 819–834<br><blockquote type="cite"><div bgcolor="#ffffff"><div><font face="MS UI Gothic" size="2">Or need (or find if possible) experimental data to tune the</font></div><div><font face="MS UI Gothic" size="2">parameter? </font></div></div></blockquote>That you'll have to do yourself. You have to parameterize your molecule </div><div>to reproduce as much as possible data from atomistic simulations and</div><div>experiments.<br><blockquote type="cite"><div bgcolor="#ffffff"><div><font face="MS UI Gothic" size="2">For my simulation the atomic simulation leads to</font></div><div><font face="MS UI Gothic" size="2">segmentation fault (Memory: 2GB) and i feel the CG is necessary.</font></div></div></blockquote>That is probably not related to the degree of desciption of your</div><div>system!<br><blockquote type="cite"><div bgcolor="#ffffff"><div><font face="MS UI Gothic" size="2"></font> </div><div><font face="MS UI Gothic" size="2">Else if Martini is not useful for more general calculation,</font></div></div></blockquote>it seems so ... <br><blockquote type="cite"><div bgcolor="#ffffff"><div><font face="MS UI Gothic" size="2">let me know the alternative approach for CG calculation</font></div><div><font face="MS UI Gothic" size="2">with GROMACS.</font> </div><div><font face="MS UI Gothic" size="2"></font> </div><div><font face="MS UI Gothic" size="2">taka</font></div><div><font face="MS UI Gothic" size="2"></font> </div>_______________________________________________<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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. 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