Vitaly V. Chaban wrote:
Payman,
Such little charge cannot produce large energies, so it seems you should run
EM first and everything will be OK with your simulation.
As far as understand non-zero charge is a resuts of averaging errors (during
grompp!), you cannot remove this warning.
That's not quite right. It results from the fact that binary floating
point operations accrue error both from inexact representation of many
exact decimal values (e.g. 0.02 has no exact representation, and so
added to itself N times, need not equal N*0.02) and from limited
precision (to 3 digits, 123 + 0.123 = 123). The former is occurring with
the sum of atomic charges in grompp. The latter can occur during the
integration, for example.
Mark
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