WARNING: Listed nonbonded interaction between particles 8099 and 8101
at distance 2.884 which is larger than the table limit 1.945 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
writing lowest energy coordinates.
Polak-Ribiere Conjugate Gradients converged to machine precision in 129 steps,
but did not reach the requested Fmax < 100.
Potential Energy = 3.4181414e+08
Maximum force = 2.2467842e+08 on atom 12096
Norm of force = 2.3482725e+06
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 304 atoms. The longest distance involved in such interactions is
2.286 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.
第二种：
Fatal error: Step 0: The total potential energy is 1.24207e+14, which is extremely high.