[gmx-users] how to extract the LJ interaction parameters from the tpr file
Mark.Abraham at anu.edu.au
Mon Feb 8 13:33:44 CET 2010
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.
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