AMBER Archive (2004)

Subject: Re: AMBER: BOND energy during minimisation

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Oct 19 2004 - 06:21:28 CDT

look at the total potential energy- it is going down even though
the bond energy goes up. if you look carefully, you'll see that the
vdw energy is going down more than the bond is going up. my guess
is that you have a close contact between atoms, and it is trying to move
them apart, stretching a bond in the process. sometimes things like this
happen, especially when you have retraints applied and the close
contact atoms can't move apart by other means.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

cailliez wrote:

> 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
>
>
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