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
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