[gmx-users] fluctuation of energy in rerun
ndhumal at andrew.cmu.edu
Wed Sep 4 02:17:21 CEST 2013
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
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
Checking the trajectory files, it seems like caused by molecule stretching
across the pbc.
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