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[lammps-users] Fix Deposit and Periodic Boundary Conditions
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[lammps-users] Fix Deposit and Periodic Boundary Conditions


From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Sun, 13 May 2018 18:47:12 -0700

Dear LAMMPS Users,

Hello LAMMPS Users. 

I would like to ask a question regarding the fix deposit command. I have a simulation box consisting of polymer chains with periodic boundary conditions on all three dimensions. When I use the fix deposit command to insert molecules into this simulation box, I am obtaining a "FENE bond too long" message. 

However, when I intentionally enlarge the size of the simulation box such that the polymer chains no longer straddle the boundaries of the box, I do not receive any errors due to bad dynamics and I see that the molecules are being properly inserted.

I was curious if I could ask on why polymer chains straddling the periodic boundaries would lead to bad dynamics when I am simply inserting molecules. I understand that molecule command does not enlarge the simulation box to make additional space for the inserted molecules thereby this command not being responsible for bad dynamics due to periodic boundary conditions.

Thank you very much!

Sincerely,

Masato Koizumi