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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