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If TRUE, the translational and rotational degrees of freedom are eliminated by
a method described in [7,8].
This may be necessary for simulations of
proteins in vacuum without any harmonic restraints or SBOUND forces. Due
to the approximation algorithm used for long range forces, conservation of
momentum is not fulfilled exactly. Via a dummy (=no flooding matrix)
lis-file flooding.lis one can specify which atom coordinates will be
used to inhibit translation or
rotation. Such dummy flooding files, together with the full flooding
files, are created by the utility program mkflood. For details see online help
information given by mkflood as well as Chapter 6.2.5.