Task qmmm dft optimization
Just Got Here
5:24:59 AM PST - Tue, Nov 18th 2014
Hi,
 I'm having some trouble runing a QM/MM optimization.

  Part of input and output files as following:

start reac

permanent_dir ./perm
scratch_dir ./data
charge -4

md
system reac_ref
end

basis
  • library "3-21G*"
end

dft
xc b3lyp
direct
iterations 50
end

qmmm
bqzone 15.0
region qm mm
maxiter 10 1000
method sd sd
ncycles 1
convergence 1.0d-3
link_atoms hydrogen
density espfit
end

task qmmm dft optimize

prepare
read reac_ref.rst
write reac_opt.pdb
end

task prepare
..............................................
The errors is below:
 convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time

---------------- ----- ----------------- --------- --------- ---------  ------

d= 0,ls=0.0,diis     1  -2647.1936558978 -6.63D+03  1.23D-01  1.28D+01    64.6

Nuclear repulsion energy =   3979.59737389340     

Bq nuclear interaction energy =  -1.09039338341947
..........................................................
d= 0,ls=0.5,diis    50  -2649.0822398429 -3.05D-04  3.81D-05  1.30D-02  2475.5

Nuclear repulsion energy =   3979.59737389340     

Bq nuclear interaction energy =  -1.09039338341947     

                  

                        Calculation failed to converge
..............................
Bq nuclear interaction energy = -1.09039338341947 
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qmmm_main                       failed qmmm_energy_gradient        0

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 current input line : 

   36: task qmmm dft optimize

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This error has not yet been assigned to a category

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Hi,
  I'm having some trouble running a QM/MM optimization on a system of a large protein.
I just simplify it into a smaller system that ATP interacted with the surrounding of the residues.I define the ATP segment as qm region and the rest as mm region.
  First,I take a task of prepare

 

  Here is the input file,pre.nw:
start reac Media:Example.ogg

permanent_dir ./perm
scratch_dir ./data

charge -2

prepare
source atp.pdb
new_top new_seq
new_rst
center
orient
modify segment 952 quantum
update lists
ignore
write reac_ref.rst
write reac_ref.pdb
end

task prepare

   Then, I use the reac.top and reac_ref.rst files obtaining from the prepare task to make optimization.I possibility set some parameters smaller so that it can quickly verify.

   

   The input file of optimization is showing below,opt.nw:
start reac

permanent_dir ./perm
scratch_dir ./data
md
system reac_ref
end

basis
  • library "6-31G"
end

dft
xc b3lyp
end

qmmm
bqzone 20.0
region qm mm
maxiter 10 1000
ncycles 2
density espfit
xyz foo
end

task qmmm dft optimize

prepare
read reac_ref.rst
write reac_opt.pdb
end

task prepare



The errors in the output file like this:

 Memory utilization after 1st SCF pass: 

          Heap Space remaining (MW):        0.00                   0

         Stack Space remaining (MW):       12.99            12989676



  convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time

---------------- ----- ----------------- --------- --------- ---------  ------

d= 0,ls=0.0,diis     1  -2625.3970221245 -6.58D+03  1.64D+01  1.78D+01   216.4

Nuclear repulsion energy =   3949.30625746002     

Bq nuclear interaction energy =   5.09231130369664     

WARNING: error on integrated density =  0.11D-05

greater than required accuracy of  0.10D-05

d= 0,ls=0.5,diis     2  -2282.8510692315  3.43D+02  4.07D+00  9.39D+02   247.5

Nuclear repulsion energy =   3949.30625746002     

Bq nuclear interaction energy =   5.09231130369664
.................


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