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I am trying for a membrane simulation of a 700 residue prot in dppc bilayer. I prepared the system.gro file but when I try to inflate and minimize it, the following warnings appear. What could be wrong, Pls guide me ?
ARNING: Listed nonbonded interaction between particles 11833 and 11837
at distance 6.212 which is larger than the table limit 2.050 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.
WARNING: Listed nonbonded interaction between particles 8280 and 8301
at distance 6.245 which is larger than the table limit 2.050 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.
Back Off! I just backed up system_inflated_em.gro to ./#system_inflated_em.gro.3#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.9288830e+18
Maximum force = inf on atom 8594
Norm of force = inf