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.
--
========================================
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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