Dear all,
I am having some troubles in get some (supposedly straightforward) relaxations
results.
I want to relax a benzene molecule in xyz format (this is a test for more
complex results).
I tried both "obminimize" and "obabel --minimize", compiling the source code
and the anaconda3 version.
In all cases I do get a different geometry with lower energy, but I can neither
get the code to stop when the criteria is reached nor obtain a convergence
message whatsoever.
$ obabel benzene.xyz -O min_benzene.xyz --minimize --steps 500 --sd --ff UFF
--log --crit 1e-4
## --crit 1e0 gives the same result, log_001.txt
$ obminimize benzene.xyz -O min_benzene.xyz --steps 500 --sd --ff UFF --crit
1e-4
In addition, In the obminimize case, I get an error message, zero charges and
alternate +/- 0.15 partial charges, as shown below.
'''
*** Open Babel Warning in ReadMolecule
Problems reading an XYZ file: Cannot read the first line.
'''
IDX CHARGE
1 0.000000
...
12 0.000000
P A R T I A L C H A R G E S
IDX CHARGE
1 -0.150000
2 0.150000
...
Could anyone explain what am I doing wrong?
Thank you
Marco
----------------------------
Marco Di Gennaro
Toyota Motor Europe
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12
benzene example
C 0.00000 1.40272 0.00000
H 0.00000 2.49029 0.00000
C -1.21479 0.70136 0.00000
H -2.15666 1.24515 0.00000
C -1.21479 -0.70136 0.00000
H -2.15666 -1.24515 0.00000
C 0.00000 -1.40272 0.00000
H 0.00000 -2.49029 0.00000
C 1.21479 -0.70136 0.00000
H 2.15666 -1.24515 0.00000
C 1.21479 0.70136 0.00000
H 2.15666 1.24515 0.00000
A T O M T Y P E S
IDX TYPE RING
1 C_R AR
2 H_ NO
3 C_R AR
4 H_ NO
5 C_R AR
6 H_ NO
7 C_R AR
8 H_ NO
9 C_R AR
10 H_ NO
11 C_R AR
12 H_ NO
S E T T I N G U P C A L C U L A T I O N S
SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
S T E E P E S T D E S C E N T
STEPS = 50
STEP n E(n) E(n-1)
------------------------------------
0 44.709 ----
10 44.27008 44.27014
20 44.26997 44.26997
30 44.26997 44.26997
40 44.26997 44.26997
50 44.26997 44.26997
...
500 44.26997 44.26997
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