Santanu Chatterjee wrote:
Hi,
I am somewhat new to gromacs. I am trying to understand how Gromacs
estimates scaled nonbonded 1-4 LJ interactions.
I learned from the manual that if gen-pairs = yes, gromacs uses the
general combination rule for nonbonded 1-4 LJ interaction
with the factor fudgeLJ. But does Gromacs calculates the scaled 1-4 LJ
interaction for all 1-4 pairs in the molecule? Or does it
do it only for the entries under the [pairs] section in topology file?
And what about Coulomb interactions?
See manual 5.3.4 and 5.7.1, and probably others.
Mark
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