[gmx-users] How to determine epsilon and sigma for particles?

[David]

On Sat, 2004-01-31 at 04:11, Albert Sun wrote:
> Dear USERS,
>  
> My question is still pending on how to find out epsilon and sigma
> to calculate LJ potential for two group of atoms.
> If I have two atoms(A1 and A2)  in a particle A, and two atoms(B1 and
> B2) in particle B. 
> I have already known the epsilon and sigma between atoms 
> A1   -   B1      ( epsilon 1   sigma 1) 
> A1  -    B2      ( epsilon 2   sigma 2)
> A2  -    B1      ( epsilon 3   sigma 3)
> A2  -    B2      ( epsilon 4   sigma 4)
>  
> Then I need to find out epsilon and sigma between  Particle A and
> Particle B
>  
> Can I use the following way ?
> Epsilon = square root of (epsilon 1^2 + epsilon 2^2 + epsilon 3^2 +
> epsilon 4^2 )
> Sigma =sigma 1+ sigma 2+ sigma 3 + sigma 4
>  
> Thanks for any advice on this.
there is no formal way. If you know how the two particle are arranged
you can fit a LJ potential to the distance (should be minimum of the
potential). However to determine epsilon, you need to knwo the well
depth. Furthermore your parameters are dependent on the distance between
A1 and A2.

Trial and error.
>  
> Best Regards
>  
> Albert
>  
>  
>  
>  
> Albert Sun <albert_sun9 at yahoo.com> wrote:
>         Hi, Dear users,
>          
>         I am not in chemical area and have a stupid question:
>          
>         In order to save computer time, I want to collapse a group of
>         molecules into a particle.
>         and then compute the L-J potential between particles.
>          
>         If I known epsilon and sigma and other bond parameters  of
>         each atom in the group of molecules, and how to find out
>         epsilon and sigma of particle in order to calculate
>         inter-particles potential?
>          
>         Thanks in Advance!
>          
>         Albert
>          
>          
>         
>         
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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