[gmx-users] fluctuation of energy in rerun

[Nilesh Dhumal]

Hello

I am running a simulation with charge and without charge for 128 pairs of
bmim-tf2n ioinc liquids.
This is the command for the original run without charge
mdrun -s gs.tpr -o gs.trr -c 0.pdb -e gs.edr -g gs.log -pd -nt 8
This is the command for the rerun with charge
mdrun -s es.tpr -o es.trr -c 0.pdb -e es.edr -g es.log -rerun gs.trr -pd
-nt 8

In the original trajectory, the energy of the system fluctuates around 5000
kJ/mol. In the rerun trajectory, the energy of the system also mostly
fluctuates around 5000 kJ/mol, but sometimes it jumps to 10^13 or 10^-13.
In the most recent run (20 ns), 16 data points out of 2000000 were
extremely large.

Checking the trajectory files, it seems like caused by molecule stretching
across the pbc.

Nilesh