1.5 Ubiquitin in a Water Box: Simulation with Periodic Boundary Conditions


cd ../1-3-box
vim ubq_wb_eq.conf

new params:


# Periodic Boundary Conditions
cellBasisVector1    42.0    0.   0.0
cellBasisVector2     0.0  44.0   0.0
cellBasisVector3     0.0    0   47.0
cellOrigin          31.0   29.0  17.5

wrapAll             on


../NAMD/namd3 ubq_wb_eq.conf > ubq_wb_eq.log &