[gmx-users] Dynamics of non-protein molecules.

[Yasen Atanasov]

Dear All,

I'm trying to use gromacs for molecular dynamics of surfactant micelles 
formation and dissolution.

While reading User's manual and some beginners tutorials some questions 
and problems occur.

1. Is there some software for creating .pdb or .top file for non 
proteins molecules like surfactants (SDS,LAS,AOT, Tween's) or I have to 
make them by hand?

2. Do I have to do something special to allow surfactant molecules to 
move freely towards each other or to take apart?

3. Does any body see any other potential pitfalls in such type of 
simulation?

Thanks.

Yasen Atanasov
post doc
Department of Chemical Engendering
Sofia University.