[gmx-users] fluctuation of energy in rerun
mark.j.abraham at gmail.com
Wed Sep 4 09:11:37 CEST 2013
Seems like a bug. Please open an issue at redmine.gromacs.org, and be sure
to mention the GROMACS version.
Why are you using -pd?
On Sep 4, 2013 2:20 AM, "Nilesh Dhumal" <ndhumal at andrew.cmu.edu> wrote:
> 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.
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