AMBER Archive (2007)

Subject: Re: AMBER: Minimization increases energy

From: saccenti_at_cerm.unifi.it
Date: Wed May 23 2007 - 12:22:33 CDT

I'm not for sure an AMBER guru, I started to use it only a few weeks ago,
so maybe I'm saying a stupid thing but your ENERGY seems to decreas from
-3E+02 at step 1 to -8.9380E+02 at step 2000 and this has a physical
meaning

Edo
>
> Dear Amber users
>
> I have taken an NMR structure of a small protein and minimized it with
> sander in implicit solvent (igb=1). My output is as follows:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -3.6789E+02 1.7668E+01 1.8766E+02 O 334
>
> BOND = 65.9631 ANGLE = 61.8355 DIHED =
> 298.1987
> VDWAALS = 44.4613 EEL = -2385.5904 EGB =
> -739.8229
> 1-4 VDW = 198.2850 1-4 EEL = 2088.7822 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1000 -8.8062E+02 7.4882E-02 5.1163E-01 C 529
>
> BOND = 18.6956 ANGLE = 61.2032 DIHED =
> 256.7138
> VDWAALS = -223.5801 EEL = -2398.7351 EGB =
> -729.0717
> 1-4 VDW = 101.0093 1-4 EEL = 2033.1486 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2000 -8.9380E+02 1.0086E-01 6.8560E-01 CE1 393
>
> BOND = 18.8494 ANGLE = 61.0641 DIHED =
> 252.0533
> VDWAALS = -228.2521 EEL = -2407.6584 EGB =
> -728.9162
> 1-4 VDW = 102.8656 1-4 EEL = 2036.1992 RESTRAINT =
> 0.0000
>
>
> etc etc with increasing energy, which then eventually begins to decrease
> again.
>
> Does anyone out there know why I have such a drastic energy increase when
> I
> only expect ever to see a decrease?
>
> My sander input file is:
>
> minimization with sander (Amber9)
> &cntrl
> imin = 1, maxcyc = 50000, drms = 0.005, ntb = 0,
> ntpr = 1000, cut = 80., igb = 1, rgbmax = 40, ncyc = 100
> &end
>
> Many thanks in advance
>
> Hayden Eastwood
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu