[gmx-users] Potential Energy problem

[Mark Abraham]

On 11/05/2010 7:55 PM, Carla Jamous wrote:
> Hi everyone,
>
> please I encountered a problem of potential energy rising suddenly
> during my simulation.
> Someone advised me to take the previous conformation of my system,
> center it in the box, minimize it & then restart my MD simulation, by
> taking the previous velocities of this conformation.
> So I did the centering and the minimization.
>
> Usually, I used to do the following for my MD run.
> tpbconv -s .tpr -extend 6000 -o .tpr
> mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc
> -e .edr -g .log
>
> However, this time I need to go from the minimized structure.
> So in order to get a .tpr file of my minimized structure (.gro), I
> created a .mdp file with gen_vel=no and did:
>
> grompp -f .mdp -c minimized.gro -p .top -o minimized.tpr
>
> After that, I tried the following:
>
> tpbconv -s minimized.tpr -extend 6000 -o .tpr
> mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc
> -e .edr -g .log
>
> and got this error message:
>
> *WARNING: This run will generate roughly 3410368410012306432 Mb of data
>
> starting mdrun 'Protein in water'
> 6 steps,  12.0 ps (continuing from step 27,  54.0 ps).

That looks like a bug. The run time from your .mdp+tpbconv is 12ps, but 
the .cpt is already past that and GROMACS is using integer arithmetic 
inappropriately to get a huge number of steps (thus large output volume 
estimate) but no actual steps occur.

If you're running GROMACS 4.0.7, please submit a bugzilla.

Mark