packmol and hyperchem can do it for u. <br><br>
<div class="gmail_quote">On Wed, Feb 16, 2011 at 4:57 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div text="#000000" bgcolor="#ffffff">On 16/02/2011 11:24 PM, oguz gurbulak wrote:
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<p style="MARGIN-BOTTOM: 0pt; TEXT-ALIGN: justify"><em><span style="FONT-STYLE: normal">Dear All</span></em>, </p>
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<p style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify">I want to generate some initial crystalline structures of my target<span style="FONT-SIZE: 8pt"> </span>molecules for md simulations. <em><span style="FONT-STYLE: normal">Are there any free softwares</span></em> to do this?</p>
</td></tr></tbody></table></blockquote><br>Some sources for obtaining initial coordinates can be found here <a href="http://www.gromacs.org/Documentation/File_Formats/Coordinate_File" target="_blank">http://www.gromacs.org/Documentation/File_Formats/Coordinate_File</a>. I doubt there is going to be software to generate "crystalline" structures (whatever you mean by that). You could get a structure and replicate it with (e.g. genconf).<br>
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<p style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify">And are there any complete sources that give the theoretical structures of organic molecules ( like hydrocarbons ) determined by the experiments and give the x-ray, neutron scattering, NMR, IR or Raman results of organic molecules apart from the articles ? Could you please share your thoughts about this issue ? </p>
</td></tr></tbody></table></blockquote><br>Theoretical structures you compute according to some model. Experimental data tends to live in original literature and lots of specialist databases. Which do you actually want? Google is your friend either way.<br>
<br>Mark<br></div><br>--<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" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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