AMBER Archive (2004)

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

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Sat Dec 18 2004 - 03:33:26 CST

Dear David and all Amber-users,

thanks for your answer.
I would like to get as close as possible to the energy calculation-results
I got from the minimisation run.

Here is a the output from my EM :

   NSTEP ENERGY RMS GMAX NAME NUMBER
   1122 -4.2410E+03 9.9105E-01 8.0228E+00 HB2 2947

 BOND = 198.9442 ANGLE = 253.7154 DIHED =
180.0488
 VDWAALS = -177.5909 EEL = -6095.5213 HBOND =
0.0000
 1-4 VDW = 84.2852 1-4 EEL = 1315.1367 RESTRAINT =
0.0000

The control data of the EM looks like that :

General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 50, ntrx = 1, ntwr
= 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
     ntf = 1, ntb = 0, igb = 0, nsnb
= 25
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut = 8.50000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 60000, ncyc = 1000, ntmin = 1
     dx0 = 0.10000, dxm = 1.00000, drms = 1.00000

The ANAL run had the following parameters :

  2. DATA CONTROL:

  
TITLE

     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 = 50 IDIEL = 0

     RCUT = 6.00 SCNB = 2.00
     SCEE = 1.20 DIELC = 4.00

     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

But I got the following energies :

         INITIAL ENERGY COMPONENTS

     TOTAL ENERGY = -3263.8021
     NON-BONDED VDW ENERGY = -1339.5276
     NON-BONDED EEL ENERGY = -9348.1178
     HBOND 10-12 ENERGY = 0.0000
     BOND ENERGY = 479.6811
     ANGLE ENERGY = 772.1824
     DIHEDRAL ENERGY = 1178.3268
     NON-BOND 14 VDW ENERGY = 993.8577
     NON-BOND 14 EEL ENERGY = 3999.7953
     BOND CONSTRAINT ENERGY = 0.0000
     ANGLE CONSTRAINT ENERGY = 0.0000
     DIHEDRAL CONSTRAINT ENERGY = 0.0000
     POSITION CONSTRAINT ENERGY = 0.0000

I played around with the cutoff value since I read something about a bug
concerning this parameter but I didn't manage to get the Total energy
cloaser to
my energy calculated by sander.

Do you know which parameter I should change in ANAL or if I could simplify
my sander configuration to get results which I could reproduce with ANAL ?

Hope you can help,

Daniel

David A. Case schrieb:

>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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