ERROR 1 [file nvt.mdp]:
Generating velocities is inconsistent with attempting to continue a
previous run. Choose only one of gen-vel = yes and continuation = yes.
when I used
gmx grompp -f nvt.mdp -c npt.gro -r npt.gro -t npt.cpt -p topol.top -o nvt.tpr
Continuation=yes and gen-val=yes are conflicting! As gen-vel=yes will assign velocities to particles randomly with Maxwell distribution for given temperature, while continution=yes asks to use previous setup (which includes velocities as well). For first molecular dynamics run (NVT relaxation) use (continution=no and gen-vel=yes. After that use continution=yes and gen-vel=no.
thanks but Actually I am going to do nvt remd simulation (300-600)K so I started with npt equilibration then followed by nvt equilibration at 600 K which I need the output structure as the initial structure for the nvt remd simulation. So how can I use velocity gen in this case?
The only time velocities are generated is immediately after energy minimization. You should preserve the velocities from the previous step by supplying the
.cpt file from the end of your NPT equilibration run to
grompp -t when preparing the new
.tpr file. Re-generating velocities randomizes the system, rendering any previous equilibration meaningless.
thanks for replying … excuse me Can I add it in npt as it always exists in nvt ?
So is there is no issue for using velocity generators with npt followed by nvt equilibration ?
I suggest you work through some simple tutorials to understand normal workflows and what the purpose of velocity generation is. Again, you should only ever generate velocities at the outset of the first stage of equilibration, regardless of what the ensemble is.