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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Received on Sat Dec 18 2004 - 09:53:01 PST
