[gmx-users] RE: [nonbond_params] section , choice of parameters

Florian Dommert dommert at icp.uni-stuttgart.de
Wed Jul 28 14:55:56 CEST 2010


 the method I know to obtain just a repulsive LJ potential is to
calculate the minimum of the potential, then set the cut-off to the
minimum and shift the whole potential by the amount of the minimum. Then
you just have a repulsive LJ interaction. However as soon as more than
one particle type is involved you will run into problems with this
method, because different cutoffs will arise. So it will be necessary to
form tables and use them.


On 28.07.10 14:31, Amir Marcovitz wrote:
> Hi Ehud,
> Did you mean that i can simply specify Sigma and Epsilon?
> The thing is that i didn't want to obtain a zero potential , but
> rather maintain the repulsive term of the LJ interaction.
> What would you specify then, for the C6 and C12 parameters?
> Amir
> On Wed, Jul 28, 2010 at 3:00 PM, Ehud Schreiber
> <schreib at compugen.co.il <mailto:schreib at compugen.co.il>> wrote:
>     Hi Amir,
>     Are you sure you’re giving the parameters indeed as C_6 and C_{12}?
>     According to the combination rule in the [ defaults ] section, you
>     may be giving the two parameters directly as sigma and epsilon;
>     sigma=0 (as well as epsilon=0) would give an identically zero
>     potential . See sections 5.3.3 and 5.7.1 in the manual (version 4.0).
>     --
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Florian Dommert
Dipl. Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70565 Stuttgart


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