<span>On 01/04/11, <b class="name">gromacs </b> <ptf1242@163.com> wrote:</span><blockquote cite="mid:7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div>Hi expert,</div>
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<div>I'd like to add sufactant to water. That means i should first get the sufactant.gro, and sufactant.top.</div></div></blockquote><br />No, you need a coordinate file for the starting point for your GROMACS work, and the pieces to combine into a .top. That might mean a coordinate file of all your surfactant molecules and matching .top file that you then solvate with genbox. Or you might want to use genconf to replicate some existing coordinate file somehow. Or you might have your starting point already and need to match a .top to it.<br /> <br /><blockquote cite="mid:7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">
<div>Someone said that we cannot get sufactant.gro and sufactant.top through grompp () sufactant.pdb. Because grompp .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.</div></div></blockquote><br />Well they (or your account of them) is wrong on what might be several points. Someone needs to understand GROMACS workflows better - perhaps by doing some tutorial material and/or reading <a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br /><br /><blockquote cite="mid:7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div ><br/></div>
<div>So that means we could not get correct .gro, .top small molecules such as inorganic or small organic molecules (such as <a class="blue12other" href="http://dict.youdao.com/search?q=ethanol&keyfrom=E2Ctranslation" target="1"><font color="#0022cc">ethanol</font></a>).</div>
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<div>So how can we get the sufactant.gro, sufactant.top?</div></div></blockquote><br />That varies widely with what raw materials exist and what the objective is.<br /><br /><blockquote cite="mid:7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div> and which force field should we choose for ordinary simulation? I know we often use ffoplass force field for solution.</div></div></blockquote><br />That's your homework, I'm afraid. See above link.<br /><br />Mark<br /><div class="mimepart text html"><br /><span title="neteasefooter"><span id="netease_mail_footer"></span></span></div>