[gmx-users] initial structures for md simulations

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 16 13:57:09 CET 2011

On 16/02/2011 11:24 PM, oguz gurbulak wrote:
> /Dear All/,
> I want to generate some initial crystalline structures of my 
> targetmolecules 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.

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