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?
Thanks, Carla On Tue, May 11, 2010 at 1:00 PM, Mark Abraham <mark.abra...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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