Dear all,
I simulated a process, and the system has two different molecules.
Molecule A with 4 different atoms (atom 1\2\3\4); Molecule B with 1 atom (atom 5).
Atom 5 has a charge of “0”, Atom 1-4 have nonzero charges.
Three kinds of pair styles are used: lj/charmm/coul/charmm 1, lj/charmm/coul/charmm 2, and lj/charmm/coul/charmm 3
lj/charmm/coul/charmm 1 is used for the inside of Molecule A: 1-1, 1-2, 1-3, 1-4, 2-2, 2-3, 2-4, 3-3, 3-4, and 4-4.
lj/charmm/coul/charmm 2 is used for the interaction between Molecule B and Molecule A: 5-1, 5-2, 5-3, and 5-4.
lj/charmm/coul/charmm 3 is used for the inside of Molecule B: 5-5.
Then I used the command :
compute Apeatompair A pe/atom pair
compute Apepair A reduce sum c_Apeatompair
compute Apeatomdih A pe/atom dihedral
compute Apedih A reduce sum c_Apeatomdih
compute pairBB all pair lj/charmm/coul/charmm 3 epair
compute pairAB all pair lj/charmm/coul/charmm 2 epair
compute pairAA pair lj/charmm/coul/charmm 1 epair
I thought that Apepair represented the pair energy on molecule A (the inside of A and the interaction between A and B), that is, the value of Apepair might be close to pairAA+pairAB. The final results show that Apepair is very different from pairAA+pairAB. I don’t know why.
And I found in the manual :“The dihedral_style charmm style calculates pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy.” What does this sentence mean? Is dihedral energy included in Apepai? BUT, Apedih still has a non-zero value.
Thank you so much
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