I am trying to do a simulated annealing with RDC and NOE restraints
but with explicit electrostatics turned on. The following param
statement seems to work ok:
parameters
nbonds
atom
nbxmod 4 {* This is set to 4 (bonds), because we are
using *}
{* internal dynamics (torsion angle
refinement). *}
wmin = 0.01 {* warning
off *}
tolerance=0.5
eps=30 cutnb=11.5 ctonnb=9.5 ctofnb=10.5 tolerance=0.5 rdie
vswitch switch
end
end
(Yes, I stole that from refine_gentle.inp)
And the electrostatics are turned on during the initial minimization
and through the first steps torsional high temperature dynamics.
However, once the cool loop starts (itype=pc6) and vanderWaals radii
start increasing, if I use the repel=$radius as in:
parameter
nbonds
cutnb=4.5 rcon=$k_vdw nbxmod=4 repel=$radius
end end
This appears to turn off the elec term in the energy function.
However, getting rid of repel results in huge VanderWaals energies
and distorted structures. Is there a way around this?
Thanks in advance,
Tom Pochapsky
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