[gmx-users] GROMACS and FENE

[David]

On Mon, 2003-09-01 at 19:23, TX wrote:
> Hi David
> FENE is primarily for the bead-spring-type polymer model. It is a bonded
> interaction. Explicitly, its standard form is:
> 
> E = -0.5 K R0^2 * ln[1 - (r/R0)^2]
> 
>   r = distance (btw two connected beads)
> 
>   coeff1 = K (energy/distance^2)
>   coeff2 = R0 (distance)
Ok, that is easy enough. I suggest you try to implement that e.g.
instead of the Morse potential. You will then only ave to edit a single
routine (morse in bondfree.c) and (ab)use the Morse parameters. If you
have a working function (with energy conservation that is) then you are
welcome to send me the source code for inclusion in a future release of
gromacs.


> 
> see Kremer, Grest, J Chem Phys, 92, p 5057 (1990)
> 
> I came across a doctoral dissertation
> http://www.ub.rug.nl/eldoc/dis/science/e.d.manias/c1.pdf which uses
> GROMACS and mentions FENE. FENE is quite popular among those who do
> coarse-grained modeling. 
> 
> Thanks,
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of David van der Spoel
> Sent: Monday, September 01, 2003 4:26 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GROMACS and FENE
> 
> 
> On Mon, 2003-09-01 at 00:33, TX wrote:
> > Dear All
> > 
> > Does GROMACS implement the FENE (finitely extendable nonlinear 
> > elastic) potential? Or has anyone modified the code to include the 
> > FENE potential? If so, I'd love to use your code/modification.
> > 
> I don't think so. Can you be more specific, I've never even heard of
> it...
> 
> 
> > Thanks,
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org 
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++