From NWChem
Viewed 1762 times, With a total of 0 Posts
|
|
|
Just Got Here
Threads 1
Posts 2
|
|
| 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
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
------------------------------------------------------------------------
qmmm_main failed qmmm_energy_gradient 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
36: task qmmm dft optimize
------------------------------------------------------------------------
------------------------------------------------------------------------
This error has not yet been assigned to a category
------------------------------------------------------------------------
|
|
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
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
.................
|
AWC's:
2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC
