AMBER Archive (2004)

Subject: AMBER: BOND energy during minimisation

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Tue Oct 19 2004 - 02:53:47 CDT

Dear all,

When I am doing minimization under constraint with AMBER7, it appears
that BOND energy is increasing dramatically, which I do not understand.
I have this same behavior with all my systems, so I guess it is not due
to it.
Moreover, when looking at the structure after the minimization, everything
looks alright.
Can anybody explain me this behavior ?

Thank you in advance,
Fabien

I put here a piece of the results and my script of minimisation :
*************************************************************************
***************************** mini.in *****************************
*************************************************************************
Minimizing the system with 25 kcal/mol restraints on the protein, 500 steps
of steepest descent and 500 of conjugated gradient
 &cntrl
   imin=1, ntx=1, irest=0, ntpr=50, ntf=1, ntb=1,
   cut=9.0, ntr=1, maxcyc=2000, ncyc=500, ntmin=1,
 &end
Group input for protein restraints: 25 kcal/mol.
 25.0
RES 1 442
END
END

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -6.3453E+05 6.9821E+01 2.0320E+04 HD12 3377

 BOND = 2343.3280 ANGLE = 1719.3282 DIHED =
4009.1606
 VDWAALS = 115269.2410 EEL = -781193.0448 HBOND =
0.0000
 1-4 VDW = 3310.9240 1-4 EEL = 20009.9011 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
     50 -8.0278E+05 4.7823E+00 7.1422E+01 H1 27755

 BOND = 39199.3901 ANGLE = 1009.7188 DIHED =
4034.7246
 VDWAALS = 79846.2988 EEL = -950377.4721 HBOND =
0.0000
 1-4 VDW = 2113.7382 1-4 EEL = 19900.2103 RESTRAINT =
1491.7613
 EAMBER = -804273.3914

   NSTEP ENERGY RMS GMAX NAME NUMBER
    100 -8.4372E+05 3.1966E+00 2.9890E+01 C 3172

 BOND = 55822.3425 ANGLE = 956.1247 DIHED =
4020.4189
 VDWAALS = 85453.6483 EEL = -1013677.6885 HBOND =
0.0000
 1-4 VDW = 2048.2648 1-4 EEL = 19880.8783 RESTRAINT =
1775.1269
 EAMBER = -845496.0109

   NSTEP ENERGY RMS GMAX NAME NUMBER
    150 -8.6229E+05 1.0001E+00 1.3839E+01 CZ 2802

 BOND = 49597.7105 ANGLE = 948.1070 DIHED =
4017.4572
 VDWAALS = 91577.3921 EEL = -1032150.6427 HBOND =
0.0000
 1-4 VDW = 2048.0445 1-4 EEL = 19880.0689 RESTRAINT =
1794.1384
 EAMBER = -864081.8625 

-- 
__________________________________________________________________
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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