[gmx-users] Self-Assembly Method

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 17 07:26:35 CEST 2007

Alif M Latif wrote:
> Hi GROMACS users,
> I'm trying to simulate number of esters together with surfactants which 
> experimentally known will self-assembly into micellar aggregates. I 
> don't know if my method is right, but i put these molecules into one pdb 
> file using VegaZZ software. Then if I successfully edited the topologies 
> and managed to run MD simulation on it, are my results valid? Or do I 
> have to specify other parameters/files/options specially for this kind 
> of interactions? Because its a self-assembly process (driven by the 
> hydrophobic effect), I believed there's no need for me to specify 
> which atoms on the corresponding molecules to interact, right? 
you need an appropriate force field, like for any simulation. See 
chapter 5 of the manual.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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