AMBER Archive (2004)

Subject: Re: AMBER: BOND energy during minimisation

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Tue Oct 19 2004 - 11:12:55 CDT

I'm assuming that all of the test cases pass, so that in fact, the behavior
you see probably _is_ something to do with how you are preparing your systems.
It does look like you have a very bad starting structure (high bond energy,
high vdW energy...) Also, getting -1 million kcal of electrostatic energy
looks wrong to me. You may want to do some intial (constrained) minimization
in vacuum (or GB) prior to solvating the system.

...good luck...dac

all the test cases pass.
I guess the big number for the energies alos come from the fact that my
system is quite big
(more than 200 000 atoms).
What is even stranger is that the BOND energy at the end of the
minimisation does not correspond
with the BOND energy of the first calculation of the following run
(although the other energies :dihedral,
vdW,... correspond). And BOND energy seems alright in the second step.
Between the two, the only change in potential energy is the reference
for the restraints (I take the
coordinates after the miniisation for reference), but I think it should
not change BOND energy.

If youo have any suggestion,
Sincerely yours,
Fabien

end of the minimisation :
   NSTEP ENERGY RMS GMAX NAME NUMBER
   2000 -9.7185E+05 2.1893E-01 4.8251E+01 CG 1415

 BOND = 72405.5692 ANGLE = 956.8872 DIHED =
4015.3298
 VDWAALS = 183187.1449 EEL = -1256122.8494 HBOND =
0.0000
 1-4 VDW = 2046.1770 1-4 EEL = 19882.0561 RESTRAINT =
1780.7859
 EAMBER = -973629.6852

beginning of heating
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 148.94 PRESS = 0.0
 Etot = -977595.9871 EKtot = 68247.9867 EPtot = ************
 BOND = 191.2806 ANGLE = 956.8872 DIHED = 4015.3298
 1-4 NB = 2046.1770 1-4 EEL = 19882.0560 VDWAALS = 183187.1449
 EELEC = ************ EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.3409E-04 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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