[gmx-users] How to add a repulsive harmonic potential

[atsutoshi.okabe at takeda.com]

>This isn't mathematically consistent, nor do I think it will be stable.  That is 
>a massive repulsion at just about any distance.  For a bit gentler approach, 
>please consider what we do with hydrophobic fragments here:

>http://pubs.acs.org/doi/abs/10.1021/ci100462t

Thank you for your advice.
I did not consider combination rule 2 for LJ potential form(I thought combination rule 1).
So I changed the [nonbond_params] parameter below. Then, it worked as I expected!
 
[ nonbond_params ]
;i   j   func      V(sigma)    W(epsilon)
 VS1  VS2   1       2.0       1.000e-03 

Best regard,
Atsutoshi Okabe