[gmx-users] restarting of shifted potential, 4.6.7 bug?

Johnny Lu johnny.lu128 at gmail.com
Tue Nov 11 15:38:04 CET 2014


I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
-4e5, which is fine.

After that, I continue the 30ns NPT with the same mdp file, except with a
longer run time (300ns).

The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now at
about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed after
step 0?

I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
grompp for both simulations.

The plot of total energies for the two simulations:
The two mdp files: http://oi58.tinypic.com/11980si.jpg

The commands that I used for continuing the simulations:

The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f
npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr

The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
npt15.mdp -c npt14.tpr -t npt14_step30000000.cpt -o npt15.tpr


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