AMBER Archive (2004)

Subject: Re: AMBER: Question concerning ANAL total energy calculation

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Mon Dec 20 2004 - 15:15:12 CST

Hi David & Amberians,

thanks for your answer. It made a mistake during pasting the results and
pasted a older result with ibelly-option.
I got the following results for sander and ANAL :

from sander :

NSTEP ENERGY RMS GMAX NAME NUMBER
9497 -1.2343E+04 9.6833E-01 1.1145E+01 H1 4853

BOND = 295.8162 ANGLE = 646.4210 DIHED = 1233.8313
VDWAALS = -2112.7547 EEL = -25900.1470 HBOND = 0.0000
1-4 VDW = 833.2051 1-4 EEL = 12661.1189 RESTRAINT = 0.0000

and from ANAL :

INITIAL ENERGY COMPONENTS

TOTAL ENERGY = -6657.8538
NON-BONDED VDW ENERGY = -2248.2623
NON-BONDED EEL ENERGY = -11164.3808
HBOND 10-12 ENERGY = 0.0000
BOND ENERGY = 295.8162
ANGLE ENERGY = 646.4210
DIHEDRAL ENERGY = 1233.8313
NON-BOND 14 VDW ENERGY = 833.2051
NON-BOND 14 EEL ENERGY = 3745.5157
BOND CONSTRAINT ENERGY = 0.0000
ANGLE CONSTRAINT ENERGY = 0.0000
DIHEDRAL CONSTRAINT ENERGY = 0.0000
POSITION CONSTRAINT ENERGY = 0.0000

It seems that the main differences are for the calculation of EEL
enrgies. I don't know how to change the
ANAL parameters to get nearly the same results.

ANAL parameters :

NTX = 1 NTXO = 0 NRC = 0
NRCX = 0 NGRPX = 20 KFORM = 1

NTB = 0 BOXX = 51.483 BOXY = 39.715
BOXZ = 57.527 BETA = 90.000

NTF = 1 NTID = 0 NTN = 1
NTNB = 0 NSNB = 25 IDIEL = 0

RCUT = 8.50 SCNB = 2.00
SCEE = 1.20 DIELC = 1.00

IMAX EBMAX EANMAX EDIHMAX ENB14MAX
1 0.00 0.10 0.10 0.10

EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
0.10 0.10 0.10 0.10 0.10

sander aparameters :

polyA-polyT 10-mer: initial minimisation prior to MD GB model
&cntrl
imin = 1,
maxcyc = 60000,
ntmin = 1,
ncyc = 1000,
igb = 0,
ntb = 0,
dx0 = 0.1,
dxm = 1.0,
cut = 8.5,
ibelly = 0,
drms = 0.1,
&end
eof

What could I change to get the same total energy from ANAL as from sander ?

Hope anyone can help.

Best wishes,

Daniel 

-- 
Dr. Daniel Wetzler
Sci. Coworker (Bioinformatics / System-Administration)
Institute for Biochemistry
University of Cologne
Zuelpicher Str. 47
room 463
D-50674 Cologne

fon : +49 221 470-7431
fax : +49 221 470-5092

David A. Case wrote:

>On Fri, Dec 17, 2004, Daniel Wetzler wrote:
>  
>
>>I'm wondering now, why the total energy calculated by sander for
>>the final step differs from the total enrgy calculated by ANAL.
>>
>>Does anyone know why this could be the case and if I should
>>change that somehow ?
>>    
>>
>
>We would need more details. Anal doesn't know anything about periodic boundary
>conditions, about GB, etc.  But for gas-phase results with no cutoff, it
>should give the same answers as sander.
>
>..dac
>
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