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

atsutoshi.okabe at takeda.com atsutoshi.okabe at takeda.com
Wed Apr 15 11:10:30 CEST 2015

>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:


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

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