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

[Justin A. Lemkul]

Yasen Atanasov wrote:
> 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?
> 

There are numerous tools for generating coordinate files, and is rather easy:

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

Coming up with sensible topologies, on the other hand, is substantially more 
difficult:

http://www.gromacs.org/Documentation/How-tos/Parameterization

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

You can do normal (unrestrained) MD to see if this accomplishes your goal, 
otherwise if you want to examine directed processes, you can use the pull code 
to bias your system in some way.

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

Too broad of a question to get any useful advice, sorry :)

-Justin

> Thanks.
> 
> Yasen Atanasov
> post doc
> Department of Chemical Engendering
> Sofia University.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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