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 ?

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.