On Tue, Mar 2, 2010 at 1:39 PM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users,
>
> Yes my system is small with around 200 atoms .
> I have another question , when I solvate my previous systems with TIP3PBOX
> .My minimization output file shows up as below with negative energy profile
> . I would like to know the reason for this .Is it related to electrostatics
> of the system .:
When you solvate the system, the majority of the energy-interactions
are water-water interactions. You have a completely different system
when it comes to computing a single-point energy, so you will get a
completely different energy. This is the main reason I said that such
energies have no physical meaning or implication. Again, it's energy
differences that are meaningful. Don't forget, though, that for
explicit solvent, the energy fluctuations will certainly differ
because you see not only the fluctuations associated with your solute,
but also the solvent.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -5.3765E+03 1.1957E+01 1.1780E+02 C3 54
>
> BOND = 83.3722 ANGLE = 111.4176 DIHED =
> 11.0838
> VDWAALS = 709.4663 EEL = -6306.5299 HBOND =
> 0.0000
> 1-4 VDW = 13.6059 1-4 EEL = 1.1321 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -6.8055E+03 2.8127E+00 7.1710E+01 C2 53
>
> BOND = 401.9747 ANGLE = 82.6036 DIHED =
> 16.6673
> VDWAALS = 720.8712 EEL = -8040.9193 HBOND =
> 0.0000
> 1-4 VDW = 12.0920 1-4 EEL = 1.2157 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -7.1563E+03 9.3186E-01 5.3313E+00 C2 53
>
> BOND = 431.8288 ANGLE = 78.8985 DIHED =
> 17.4077
> VDWAALS = 826.8493 EEL = -8524.4105 HBOND =
> 0.0000
> 1-4 VDW = 11.7925 1-4 EEL = 1.2895 RESTRAINT =
> 0.0000
>
> Your help is highly appreciated .
>
> Thanks
> John.
>
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 02 2010 - 11:00:04 PST
