Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service.
I do not do polymer simulations, nor do I have any real clue as to how to help
you, aside from suggesting the following, which may or may not be relevant:
http://www.gromacs.org/Documentation/How-tos/Polymers
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
I am CC'ing this message to the list. Please keep all further posts there, as
perhaps someone can actually help you.
-Justin
Björn Nadrowski wrote:
Hi Justin,
I just found out that you are simulating polymers using gromacs.
I would like to do the same stuff, but from a much less molecular angle.
I am the only one here that does that stuff, so I have to jump through all the loops myself,
and the gromacs loop is really tiny and hard to jump through.
Ideally, I would just like to define my polymer as a succession of identical nodes,
that have a user(i.e. defined by me) interaction potential (essentially hard core repulsion with an
intermedeiate attractive regime), some 3-node angle stiffness term, friction (no water! Just the polymers with friction!),
position restraints (all bonds between the nodes should be constrained to have the same length), and
some boundary conditions.
How would I go about that?
I have scanned the documentation, but I am beaten to death by its volume, where
most of it concerns stuff I am not
interested in. Ideally, I would like to represent my nodes as some kind of idealistic atom with said interactions.
However, I do not find the part where I define such an atom, or how to do that.
Can you point me to some source where I might get a nice simple tutorial of how to define such an elementary node, and its interactions?
Thanks, Bjoern
--
========================================
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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