Should I be worried about this warning , or should I ignore with -maxwarn

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
I generated a final tpr file with mdp file in the step prior to start the final production run and got two warning , The first one I understand is because I skipped equilibration step but the second one I am not quite getting , Kindly help .
The warnings:
WARNING 1 [file 0_20ns.mdp]:
You are generating velocities so I am assuming you are equilibrating a
system. You are using Parrinello-Rahman pressure coupling, but this can
be unstable for equilibration. If your system crashes, try equilibrating
first with Berendsen pressure coupling. If you are not equilibrating the
system, you can probably ignore this warning.

WARNING 2 [file unknown]:
There are atoms at both ends of an angle, connected by constraints and
with masses that differ by more than a factor of 13. This means that
there are likely dynamic modes that are only very weakly coupled. To
ensure good equipartitioning, you need to either not use constraints on
all bonds (but, if possible, only on bonds involving hydrogens) or use
integrator = sd or decrease one or more tolerances:
verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
4 or SHAKE tolerance <= 1e-05

2

@jalemkul , sir kindly help me understand the warnings, are they fatal?

3

Warnings indicate likely problems with the physics of the simulations. The first is trivial to solve - don’t use Parrinello-Rahman for a simulation in which velocities are generated. The second is more challenging and depends on the force field that’s being used but the suggestions provided should give you a solution.