[gmx-users] how to extract the LJ interaction parameters from the tpr file

[Mark Abraham]

On 08/02/10 23:07, Baofu Qiao wrote:
> Hi Mark,
>
> Thanks for your reply!
>
> I want to use the pre-saved trajectory.  Based on the distance criteria,
> calculate the Coulomb and LJ interaction. However, I don't know the data
> structure related with the LJ parameters. Do you have related knowledge?

The pairlist construction makes all this fairly messy. If you can do it 
with -rerun, do it.

> The mdrun -rerun might be impossible for me, because I want to calculate
> the energy terms based on the distance, which is not the cutoff distance
> in the simulations, but one from RDF calculation.

That's fine. You can do mdrun -rerun with a .tpr that encodes a distinct 
model physics from one that made the simulation - that's one thing it is 
for. Thus you can pick your LJ model at will.

Mark