On 05/12/10 19:41, Justin A. Lemkul wrote:
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?
Hi Bjoern,
Your experience is much like mine -I am actually doing something very
similar, a coarse grain to model proteins which has very very similar
features (I even suspect we're starting from the same literature, given
the description). My advice is:
- Read the documentation. Multiple times. Understand it. *All* of it
concerns stuff you *will* be interested in (apart perhaps some specific
analysis tool, but even there...). Yes, it's long, but there's no hope
of going anywhere without knowing it.
- Look at how residues and force fields are defined. Learn to create
your own force field. The easiest thing is probably taking an existent
force field, duplicate it and then work on the copy customizing it to
your liking (That's what I did).
- Also, look at how protein residues are defined for use with pdb2gmx
etc. - even if you are designing a non-protein polymer, it all basically
starts from there, you then edit the residues etc. until you get the
"unit" you want.
- Learn about tables and tabulated potentials if VdW functions are not
enough.
- Learn about charge groups, energy groups etc.
- Remember that hardcore repulsion doesn't play well with MD
integration: you'll spend a lot of time tuning it to be stiff enough but
not too much to make your system explode
- About friction, do you mean Langevin dynamics?
- Do a lot of tests :)
It's very general advice, I know, but there's no real tutorial for such
a thing, every custom model is... custom, and everyone, wanting
different things, is quite on its own.
Best of luck! It took me about 1 - 1.2 years to get the model begin to
work, so be patient and don't despair!
cheers,
M.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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