Hi all,
I have a long of molecule of 155 atoms for which i want use UFF (universal force field) parameters. In avogadro we can optimize the geometry of the structure using UFF parameters. My question is as follows:
- Is there any way to print the UFF parameters used by avogadro, so that i can use it other MD engines?
- Can I get theoretical PXRD pattern from avogadro?
I could be very thankful if some one could provide some insight regarding above queries.
Thanks for reply in advance,
Mohan
Avogadro uses Open Babel for force field calculations. You can automate geometry optimizations using UFF in Open Babel. You could, in principal print the UFF parameters with Open Babel by increasing the level of verbosity - that’s probably easier addressed on the Open Babel discussion lists.
The key question for printing parameters is what format you’d want them and what MD engines you use.
Can you ask the second question in a separate thread (to make it easier for people to find)?
Hi
I put an Avogadro extension at https://github.com/brhr-iwao/libavogadro1cp2k. This extension can be used to print a molecular UFF parameter in CHARMM parameter file format.
Now I am still in making it, I should notify in advance that there are many bugs in it
and I can’t warrant the correctness of the print.
This extension also provides a CP2K input deck.
CP2K can calculate coherent X-ray diffraction spectrum.
My CP2K input generator can not yet generate a XRD calculation input,
But you can get an input for it by editting a little of the generated deck.
The following is a simple example input for methane, which was made
by adding the two line
&XRAY_DIFFRACTION_SPECTRUM ON
&END
to FORCE_EVAL%DFT%PRINT section of a generated QS input
&GLOBAL
PROJECT myProject
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
MULTIPLICITY 1
BASIS_SET_FILE_NAME GTH_BASIS_SETS
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
NGRIDS 4
CUTOFF 30
&END MGRID
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&PRINT
&XRAY_DIFFRACTION_SPECTRUM ON
&END XRAY_DIFFRACTION_SPECTRUM
&END PRINT
&END DFT
&SUBSYS
&COORD
C -1.34785 1.36445 0.00000
H -0.27785 1.36445 0.00000
H -1.70451 1.79900 -0.91042
H -1.70452 1.93562 0.83154
H -1.70452 0.35874 0.07888
&END COORD
&KIND H
BASIS_SET SZV-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND C
BASIS_SET SZV-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&CELL
ABC 10 10 10
PERIODIC XYZ
&END CELL
&END SUBSYS
&END FORCE_EVAL
-------------------------------------------------------------------
And the following is the calculation result (partial):
#
# Coherent X-ray diffraction spectrum
#
# Soft electronic charge (G-space) : -8.0017701460
# Hard electronic charge (G-space) : 0.0000000000
# Total electronic charge (G-space): -8.0017701460
# Density cutoff [Rydberg] : 30.0000000000
# q(min) [1/Angstrom] : 0.6283185307
# q(max) [1/Angstrom] : 19.5890331337
# q(max) [1/Angstrom] (requested) : 20.0000000000
# Number of g-vectors (grid points): 46656
# Number of g-vector shells : 592
# Grid size (a,b,c) : 36 36 36
# dg [1/Angstrom] : 0.628 0.628 0.628
# dr [Angstrom] : 0.278 0.278 0.278
#
# shell points q [1/A] <|F(q)|^2> Min(|F(q)|) Max(|F(q)|) <|F(q)|>^2 <|F(q)|^4>
1 1 0.000000 64.028325 8.001770 8.001770 64.028325 4.099626E+03
2 6 0.628319 53.022995 7.250621 7.303019 53.022491 2.811545E+03
3 12 0.888577 43.952134 6.559679 6.725891 43.949190 1.932310E+03
4 8 1.088280 36.468773 5.927232 6.125892 36.463541 1.330730E+03
5 6 1.256637 30.538574 5.436735 5.590273 30.534343 9.331181E+02
:
:
588 6 18.564660 0.000128 0.007818 0.013962 0.000122 1.937312E-08
589 12 18.870488 0.000037 0.001217 0.009203 0.000027 2.494650E-09
590 6 18.891397 0.000065 0.006357 0.009476 0.000063 4.624287E-09
591 6 19.233117 0.000018 0.003684 0.004815 0.000018 3.489071E-10
592 1 19.589033 0.000001 0.000943 0.000943 0.000001 7.908202E-13
-------------------------------------------------------------------
The 3rd column is q vector (q=4π sin(θ/2)/λ) [1/A] and the 4th column<|F(q)|^2> is coherent X-ray scattering intensity. Thus plotting them with 2d plotting software such as gnuplot gives the coherent X-ray diffraction spectrum.
Hope this helps.
Aoyama Iwao