> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2500 -1.5472E+05 5.3890E-01 3.1856E+01 H1 26328
>
> BOND = 11197.6011 ANGLE = 293.1576 DIHED = 878.3573
> VDWAALS = 28137.6817 EEL = -191368.2955 HBOND = 0.0000
> 1-4 VDW = 343.3582 1-4 EEL = -4205.1036 RESTRAINT = 0.0000Ħħ
>
> I think "VDWAALS = 28137.6817 , 1-4 VDW = 343.3582" it is high which
> represents the bad contacts in water and RNA and cannot drop when run
> minimisation stage 2. Please see the the minimisation stage 2 results:
(1) The absolute energies are somewhat meaningless, except that positive
bond/angle/dihedral definately mean deviation from the equilibrium value.
(2) Positive VDW is unfavorable, but remember that this is a balance among
interactions. If you have oppositely charged atoms, since electrostatics
are shorter ranged (1/distance) these are favored. To favor the
electrostatics, atoms will slightly overlap (leading to positive vdw). It
is all a question of balance.
(3) The magnitude of electrostatics/vdw will depend on the water model,
force field, etc. If you had run these with the TIP3SP model (with a
small vdw on the hydrogen), the vdw energy would likely be even higher.
Much of the very negative electrostatics and positive vdw is due to the
water.
(4) Relative energies are more relevant; have the vdw and electrostatic
energies stabilized?
-- tec3
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Received on Sun May 11 2008 - 06:07:20 PDT
