[gmx-users] Potential Energy problem

Carla Jamous carlajamous at gmail.com
Tue May 11 14:45:42 CEST 2010

Thank you Mark,

I'm running gromacs 4.0.3., so I don't know if I should submit a bugzilla.
Please Do you know another way to restart my MD run?


On Tue, May 11, 2010 at 1:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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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