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<p>Okay, I looked at the first paper. As Abhijit said, you can manipulate any part of your input coordinates by using something like packmol. In addition, pymol and GMX itself (editconf) provides means for translation and rotation of your choosing. I think VMD has this functionality as well, although I only use it as a viewer.</p>
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<p>There's little to add at this point: learn the tool(s) of your choice and use them to manipulate your coordinates.</p>
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<p>Alex</p>
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<p>GR> Thank you Alex</p>
<p>GR> First of all it is better to say that I am a beginner. I follow two papers</p>
<p>GR> for my project. The authers are ''Tumala'' and ''Samalkorpi'' .</p>
<p>GR> My surfactants are mixture of CTAB and SDS. In these two papers surfactants</p>
<p>GR> were put perpendicular on the graphene sheet. because if I put surfactants</p>
<p>GR> random in the box it will take a alot of time for surfactants to transfer</p>
<p>GR> to the graphene sheet. The simulation method in the papers is GROMACS but</p>
<p>GR> authors did not mention how they loacted surfactants on the graphene sheet.</p>
<p>GR> I have written the link of the papers. I knew that it is not specifically</p>
<p>GR> Gromacs but I would like to know with which software I can make this</p>
<p>GR> change on configuration.</p>
<p>GR> http://pubs.acs.org/doi/abs/10.1021/jp077636y</p>
<p>GR> http://pubs.acs.org/doi/abs/10.1021/jp077678m</p>
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<p><span class=rvts7>Hi,</span></p>
<p><span class=rvts7>I am not sure anyone will be able to help, because this isn't really about Gromacs. Can you please clarify who "they" are and what exactly you mean by "perpendicular" when talking about surfactants? Also, what are those surfactants? Anyway, a reference to a representative paper and some instructions on where to quickly see what you're talking about would be nice. Once again, this isn't something Gromacs-specific.</span></p>
<p><span class=rvts7>Alex</span></p>
<p><span class=rvts7>On May 15, 2015 9:17 AM, "Golnaz Roudsari" <</span><a class=rvts8 href="mailto:golnaz.chem@gmail.com">golnaz.chem@gmail.com</a><span class=rvts7>> wrote:</span></p>
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<p><span class=rvts7>Dear gmx-user</span></p>
<p><span class=rvts7>I want to simulate graphene and surfactants in water. In most of the paper</span></p>
<p><span class=rvts7>they put surfactants perpendicular on the graphene sheet. I have problem in</span></p>
<p><span class=rvts7>initial configuration. I do not know how They put them perpendicular on the</span></p>
<p><span class=rvts7>graphene sheet. I can not put them random in my box because I do not have a</span></p>
<p><span class=rvts7>perfect system for more than 50 ns MD run.</span></p>
<p><span class=rvts7>Thank you in advance</span></p>
<p><span class=rvts7>Golnaz Vahabpour</span></p>
<p><span class=rvts7>--</span></p>
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<p><span class=rvts9>-- </span></p>
<p><span class=rvts9>Best regards,</span></p>
<p><span class=rvts9> Alex </span><a class=rvts10 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
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