Inquiry on fx, fy and fz and skin distance

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1

Dear Dr. Axel Kohlmeyer,

Hello Dr. Kohlmeyer. I was curious if I could ask a question regarding the forces (fx, fy, fz) acting on a given atom specified in the dump file.

I modeled a simulation box containing polymer chains where I define two interatomic potentials, pairwise potential (LJ potential) between non-connected atoms and bond potential (FENE potential) applied between connected atoms. The portion of the script look as the following:

neighbor 0.38 bin
neigh_modify delay 1
pair_style lj/cut 2.4
bond_style fene
special_bonds lj 0.0 1.0 1.0

pair_coeff * * 1.0 1.0 2.4
bond_coeff * 30.0 1.5 1.0 1.0

If fx, fy, and fz are the resultant forces acting on each atom due to both LJ potential and pairwise FENE potential, then, would atoms feel forces due to LJ potential from neighboring atoms if their interatomic distance exceeded the 2.4 cutoff distance but within the skin distance defined by the neighbor command.

Although the skin distance is used to store the neighboring atoms in a Verlet list, can the skin distance also be used to extend its reach to other the atoms to feel forces from neighboring atoms?

Thank you.

Sincerely,

Masato Koizumi

2

It sounds like you want to run the dynamics for forces based on a short cutoff, but at the same time output forces based on a larger cutoff. This does not really make much sense, but you could achieve it by first running the simulation with the short cutoff, dumping x,y,z coordinates periodically and then rerunning the force calculation on each snaphot using the rerun command, calculating forces using the longer cutoff and dumping them to a separate file.