Hi, Thomas,
Thanks for your explain.
I guess maybe the problem caused by high VDW, but not sure. I try lots of methods such as run short MD with shorter time steps (0.5fs or 1fs), but the same problem happens. Maybe my initial structure builded by nucgen has a serious problem, but I can not find the reason.
Regards,
Ouyang
----------------------------------------
> Date: Wed, 7 May 2008 21:51:55 -0600
> From: tec3.utah.edu
> To: amber.scripps.edu
> Subject: RE: AMBER: Ewald error estimate
>
>
>> 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 = 0.0000”
>>
>> 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 - 06:07:21 PDT
