Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log
But in my em.mdp, I kept: gen_vel = yes So is my simulation correct or does it generate velocities each time? I mean, what is meaningful: gen_vel or grompp -t -e ? Thank you Carla
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