[gmx-users] Re: polymer simulations in gromacs

[Justin A. Lemkul]

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
> 
> 

-- 
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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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