Gen_vel=no and continuation=false

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1

GROMACS version: 2023.4
GROMACS modification: No
Hi!
I’m performing a 10μs simulation divided into 50 simulations of 200ns each. I set ‘gen_vel=no’ in the mdp file, but I didn’t include ‘continuation=yes’. The simulations are working, but I can’t understand how GROMACS generates velocities. Also i didn’t include the grompp -f .cpt flag.

gmx grompp -f md_0mV.mdp -c md_0mV-001.gro -r md_0mV-001.gro -p …/system_60_mol.top -n …/index.ndx -o md_0mV-002.tpr
gmx mdrun -v -deffnm md_0mV-002 -ntmpi 1 -nt 10 -nb gpu
Thank you everybody!

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The continuation option does not affect velocity generation. It controls whether the initial coordinates and velocities are constrained and whether the state of thermo- and barostat, when present, are taking from the checkpoint file (which you do not pass).

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I had a similar question and wanted to confirm, if the mdp file has set gen_vel=no and the grompp command doesn’t include a checkpoint file, are initial velocities still assigned to match the temperature set by the thermostat? In that case, is gen_vel meant for a more specific purpose other than just setting the initial velocities or is it automatically set to yes if no checkpoint file is provided?

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Only gen_vel generates new velocities. Several other file formats also support velocities, such as gro and trr. When the no velocities are provided and gen_vel=no, the initial velocities will all be zero.