Hi everyone,<br><br>please I encountered a problem of potential energy rising suddenly during my simulation.<br>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. <br>
So I did the centering and the minimization. <br><br>Usually, I used to do the following for my MD run.<br>tpbconv -s .tpr -extend 6000 -o .tpr<br>mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc -e .edr -g .log<br>
<br>However, this time I need to go from the minimized structure.<br>So in order to get a .tpr file of my minimized structure (.gro), I created a .mdp file with gen_vel=no and did:<br><br>grompp -f .mdp -c minimized.gro -p .top -o minimized.tpr<br>
<br>After that, I tried the following:<br><br>tpbconv -s minimized.tpr -extend 6000 -o .tpr<br>
mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc -e .edr -g .log<br><br>and got this error message:<br><br><b>WARNING: This run will generate roughly 3410368410012306432 Mb of data<br><br>starting mdrun 'Protein in water'<br>
6 steps, 12.0 ps (continuing from step 27, 54.0 ps).<br><br>nodetime = 0! Infinite Giga flopses!<br> Parallel run - timing based on wallclock.</b><br><br><br>Please does anyone have a solution?<br><br>Thanks,<br>Carla<br>
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