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

Albert Sun albert_sun9 at yahoo.com
Sat Jan 31 04:13:01 CET 2004

```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.

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?

Albert

---------------------------------
Do you Yahoo!?
Yahoo! SiteBuilder - Free web site building tool. Try it!

---------------------------------
Do you Yahoo!?
Yahoo! SiteBuilder - Free web site building tool. Try it!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040131/e352920d/attachment.html>
```