Charge density map problem

Clicked A Few Times

2:52:04 AM PST - Fri, Dec 14th 2012

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

Forum Vet

12:24:09 PM PST - Mon, Dec 17th 2012
Check geometry of the system...
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

Forum >> NWChem's corner >> General Topics