Dear Adrian,
Thank you for your response. my problem is about r. Actually, does R means simply atomic initial positions OR distance from its pair atom (Ra-Rb) in the neighbor list ?
Sincerely,
Dear Adrian,
Thank you for your response. my problem is about r. Actually, does R means simply atomic initial positions OR distance from its pair atom (Ra-Rb) in the neighbor list ?
The first term is a kinetic energy contribution for atom I. See details below on how the specified temp-ID can affect the velocities used in this calculation. The second term is a pairwise energy contribution where n loops over the Np neighbors of atom I, r1 and r2 are the positions of the 2 atoms in the pairwise interaction, and F1 and F2 are the forces on the 2 atoms resulting from the pairwise interaction. The third term is a bond contribution of similar form for the Nb bonds which atom I is part of. There are similar terms for the Na angle, Nd dihedral, and Ni improper interactions atom I is part of. There is also a term for the KSpace contribution from long-range Coulombic interactions, if defined. Finally, there is a term for the Nf fixes that apply internal constraint forces to atom I. Currently, only the fix shake and fix rigid commands contribute to this term.