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

Johnny Lu johnny.lu128 at gmail.com
Tue Nov 11 15:44:57 CET 2014

by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i
ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum &

On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi.
> 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:
> http://oi60.tinypic.com/ddmejd.jpg
> 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
> Thanks.

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