From NWChem
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| 2:52:04 AM PST - Fri, Dec 14th 2012 |
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When I finished QM/MM optimization, I wanted to get the charge density map, so I used "dplot" to generate gaussian cube file.
But when I open the cube file, I found that the volumetric datas in cube file were both zero. Part of the cube file is as follow:
CHARGE
Total Density
45 -18.897265 -18.897265 -18.897265
116 0.328648 0.000000 0.000000
116 0.000000 0.328648 0.000000
116 0.000000 0.000000 0.328648
6 6.000000 16.228967 -0.075589 42.755050
1 1.000000 17.572562 -0.995886 44.021167
1 1.000000 15.616696 1.710202 43.605427
8 8.000000 14.129481 -1.727210 42.397892
1 1.000000 13.458628 -1.370051 40.721705
6 6.000000 1.494773 -2.621050 33.004064
1 1.000000 -0.054802 -3.637723 32.100775
6 6.000000 3.896615 -4.208420 32.652575
1 1.000000 3.715201 -6.009329 33.669248
1 1.000000 4.265112 -4.665733 30.674032
1 1.000000 5.567133 -3.233321 33.399017
6 6.000000 0.895730 -2.352709 35.832984
1 1.000000 0.650066 -4.212199 36.713596
1 1.000000 2.430188 -1.394618 36.849657
1 1.000000 -0.848487 -1.286903 36.161797
17 17.000000 6.867264 -11.323238 40.956031
6 6.000000 8.038894 -8.554790 39.646451
6 6.000000 8.123932 -8.396053 37.017842
6 6.000000 9.015883 -6.224757 35.840543
6 6.000000 9.775553 -4.229207 37.361773
7 7.000000 10.726085 -1.893505 36.212819
8 8.000000 11.844802 -0.425188 37.622555
8 8.000000 10.357588 -1.559024 33.994281
6 6.000000 9.694294 -4.353929 39.967705
6 6.000000 8.896830 -6.555459 41.160122
6 6.000000 8.944073 -6.619710 43.994711
8 8.000000 7.281114 -7.615596 45.243820
7 7.000000 10.979308 -5.453749 45.079413
6 6.000000 11.066235 -4.922736 47.692904
6 6.000000 11.948737 -2.556799 48.462023
6 6.000000 11.956296 -1.942638 51.016932
6 6.000000 11.096471 -3.656620 52.823511
6 6.000000 10.293337 -6.041454 52.046833
6 6.000000 10.285779 -6.687740 49.497593
1 1.000000 7.490874 -9.987202 35.895345
1 1.000000 9.106590 -6.066020 33.799639
1 1.000000 10.179954 -2.713647 41.080753
1 1.000000 12.235976 -4.482430 43.975813
1 1.000000 12.585575 -1.224542 47.033390
1 1.000000 12.664944 -0.115273 51.612196
1 1.000000 11.098361 -3.159622 54.813392
1 1.000000 9.673507 -7.417175 53.437671
1 1.000000 9.667838 -8.535892 48.892880
1 1.000000 17.130663 0.302239 40.954338
1 1.000000 1.682347 -0.793541 32.149262
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00
The input file is:
echo
start 3E00
memory total 6000 Mb
prepare
read 3E00_opt.rst
write 3E00_opt_bak_1.rst
end
task prepare
basis
* library 6-31g*
end
driver
maxiter 400
end
scf
singlet
rhf
maxiter 400
direct
print "parameters"
print "information"
print "convergence"
end
dft
xc m06-2x
iterations 400
print "coulomb fit"
print "intermediate energy info"
print "intermediate evals"
end
md
system 3E00_opt
sd 2000 init 0.01 min 1.0e-5 max 0.05
cutoff 1.0 qmmm 1.0
noshake solute
msa 6000
mwm 10000
print step 1 extra
print energies 1
end
qmmm
region qmlink mm_solute solvent
method bfgs sd sd
maxiter 400 2000 2000
ncycles 60
density espfit
end
dplot
TITLE CHARGE
vectors 3E00.movecs
LimitXYZ
-10.0 10.0 115
-10.0 10.0 115
-10.0 10.0 115
spin total
gaussian
output 3E00-charge-density.cube
end
task qmmm dft energy
task qmmm dplot
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Edited On 2:53:14 AM PST - Fri, Dec 14th 2012 by Lmyiop
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Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Vet
Threads 5
Posts 598
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| 12:24:09 PM PST - Mon, Dec 17th 2012 |
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Check geometry of the system...
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From the cube file output it is clear that your molecule is not in the -10 to 10 angstrom reference frame. See for example:
6 6.000000 16.228967 -0.075589 42.755050
1 1.000000 17.572562 -0.995886 44.021167
1 1.000000 15.616696 1.710202 43.605427
8 8.000000 14.129481 -1.727210 42.397892
This first part of the cube file are the atoms. You should be able to look at this in the output too. Hence, you should check the physical space the atoms are in and set your cube coordinates accordingly.
Bert
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