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I need to do molecular dynamics simulation of cyclodextrine molecules for a project and I am searching for an open source solution that can be used. I found LAMMPS to be quite well maintained and wanted to use it for the MD simulation. However, after spending now around 10 hours trying to figure out how to specify an input geometry for a LAMMPS calculation, I am stuck. Has anyone experience with doing MD simulations of molecules using LAMMPS? Given an input structure in standard .xyz format, how do I start a LAMMPS MD calculation on it?

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    $\begingroup$ Obviously this discussion was not going anywhere, so I took the liberty to clear it. I understand that you are frustrated with the program, but I am quite certain, that if you don't add more context and what you have tried so far, this question will get closed (It already has 3 CV). I personally think it is also important to mention, that there is no such thing as a standard xyz format. $\endgroup$ – Martin - マーチン Feb 9 '17 at 14:22
  • $\begingroup$ @Martin-マーチン Thanks : ) Yes, xyz is not really a standardized file format but it is still simple enough that OpenBabel almost never fails on it and that is enough for me. Surely, cml might be a real standard but is also more complicated... $\endgroup$ – logical x 2 Feb 9 '17 at 15:33
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    $\begingroup$ @Martin-マーチン OpenBabel does specify a standard, FWIW. Agree it's not universal or the only way to specify a geometry, though. $\endgroup$ – hBy2Py Feb 9 '17 at 15:33