[gmx-users] GROMACS and FENE

[TX]

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)

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,
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. 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
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