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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
