[gmx-users] LJ parameters

[Erik Lindahl]

Valentin Gogonea wrote:

> Dear Gromacs users,
>
> There are LJ c6 and c12 parameters both in [atomtypes] and 
> [nonbond_params] sections of ffgmxnb.itp file. Which of them are used 
> and under what circumstances? Is this described somewhere in the manual?

Check the topology section;

In short, the parameters in [atomtypes] are the default ones for each 
atom species (e.g. A-A or B-B interaction). When we have combinations 
like A-B you can either use combination rules, or explicitly specify the 
parameters to use for e.g. A-B interactions.

The same thing goes for [ pairtypes ] (i.e. 1,4 - interactions). They 
can be generated by scaling the normal parameters (fugde factors), or 
you can specify them manually.


Cheers,

Erik