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

Baofu Qiao qiaobf at gmail.com
Mon Feb 8 13:07:54 CET 2010

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 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.

Baofu Qiao

Mark Abraham wrote:
> On 08/02/10 21:03, Baofu Qiao wrote:
>> Hi all,
>> I want to calculate the non-bonded interactions (LJ+Coulomb) between two
>> sub-groups when they are within the cutoff distance. The sub-groups are
>> only parts of the whole energy groups used in my .mdp file. Given the
>> partial charges of the atoms involved are easy to get from the
>> "top.atoms.atom[index[i]].q",   I have no idea how to get the LJ
>> parameters of the atoms?
>> Does anyone know how to get them from the top.atoms.atomXXX? Or is there
>> some similar code to calculate such energies?
> If you want them calculated mid-simulation, then you'll have to find
> the relevant data structure.
> Otherwise, define useful energy groups, and calculate the terms from
> frames in a saved trajectory using mdrun -rerun. Get the data from the
> resulting .edr with g_energy in the usual way.
> Mark

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