[gmx-users] Potential Energy problem

Carla Jamous carlajamous at gmail.com
Tue May 11 11:55:30 CEST 2010

Hi everyone,

please I encountered a problem of potential energy rising suddenly during my
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).

nodetime = 0! Infinite Giga flopses!
    Parallel run - timing based on wallclock.*

Please does anyone have a solution?

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