[gmx-users] initial structures for md simulations

leila separdar separdar.leila at gmail.com
Thu Feb 17 12:57:58 CET 2011

packmol and hyperchem can do it for u.

On Wed, Feb 16, 2011 at 4:57 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 16/02/2011 11:24 PM, oguz gurbulak wrote:
>   *Dear All*,
> I want to generate some initial crystalline structures of my target molecules
> for md simulations. *Are there any free softwares* to do this?
> Some sources for obtaining initial coordinates can be found here
> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File. 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).
>   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 ?
> 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.
> Mark
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