I have portlandite crystal parameters (a=b = 3.585 c= 4.871) with P-3m1 space group. I need to make cleaved surface using this crystal. Atomic position has taken from Henderson D M, Gutowsky H S American Mineralogist 47 (1962) 1231-1251 paper.
I tried to built crystal and add QEq charges from crystal builder in Material Studio 5.5 and then did geometry optimization using UFF force field in the forcite module. Density value (2.5 g/cc) was near to actual value (2.2 g/cc). However lattice values (gopt values a=b=2.98, c=6.18) are way from actual lattice value (a=b=3.85, c= 4.87).
Also I optimized this crystal using DFT using DMol3 in material studio and tried use its charges but results was not satisfactory.
How I can get charges for atoms in crystal? What is a basic procedure for getting optimized crystal?
Your input is valuable to me.
Try this CIF and see how, I've used material studio before and never face such a problem with it.
Dear Michael,
Thanks for your response. I used cif files before for crystal construction but when I geometry optimized it using UFF, it was not giving correct crystal density and lattice parameters. When, I used your cif file and applied Qeq charges, after geometry optimization with UFF, lattice parameter changed to a: 2.951079 A b: 2.951079 A c: 6.131887 A and density went up to 2.8 g/cc.
Do you have any suggestion?
In the geometry optimization, what is the alogarithm that u used?
Try to optimize the geometry without use the current charges first, then u can do QEq for the optimization one. In the forcite QEq, inital charges use Current.
Did the attachment is the result u looking at?
Michael,
I was using SMART algorithm for geometry optimization. I took your cif file and wo connecting any bond, geometry optimized using forcite UFF (current charges were 0.000 for all atoms). Optimized cell parameter were a=b=4.90 and c=5.98 and density=1g/cc.
Then I applied Qeq charges on optimized molecule and geometry optmized with same procedure (UFF, electrostatic-Ewald, van der Waal- atom based, Smart , ultra fine) energy reduced to -156 kcal/mol and parameters were a=b= 4.18, c= 6.57 and density=1.25g/cc. For both geometry optimization 'cell optimized' option was checked.
I was not getting the output that you were showing in the attachment. Should I connect the bonds for geometry optimization ?
Thank you.
I saw that i'm not use the 'cell optimized'.
Yes u rite if we use UFF the posibility end up with density of 1.25 - 1.50 g/cc.
Here I use a COMPASS27, with density of 2.08 g/cc
Forcite
-------
Task : Geometry Optimization
Version : 6.0
Build date : Dec 8 2011
Host : maykel-PC
Threads : Scalar
Operating system : Windows
Task started : Tue Jul 15 12:59:16 2014
---- Geometry optimization parameters ----
Algorithm : Smart
Convergence tolerance:
Energy : 0.001 kcal/mol
Force : 0.5 kcal/mol/A
Maximum number of iterations : 500
External pressure : 0 GPa
Motion groups rigid : NO
Optimize cell : YES
---- Energy parameters ----
Forcefield : COMPASS27
Electrostatic terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 12.5 A
Spline width : 1 A
Buffer width : 0.5 A
van der Waals terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 12.5 A
Spline width : 1 A
Buffer width : 0.5 A
Energy contributors with missing parameters:
Bond Stretch : (ca2o ca2o), (ca2o o)
Angle Bend : (ca2o ca2o ca2o), (ca2o ca2o o), (o ca2o o)
Torsion : (ca2o ca2o ca2o ca2o), (ca2o ca2o ca2o o),
: (ca2o ca2o o ca2o), (ca2o ca2o o h1o), (ca2o o ca2o o),
: (h1o o ca2o o), (o ca2o ca2o o)
Energy contributors using automatic parameters:
Angle Bend : (ca2o o ca2o), (ca2o o h1o)
---- Initial structure ----
Total enthalpy : -363.207420 kcal/mol
External pressure term : 0.000000 kcal/mol
Total energy : -363.207420 kcal/mol
Contributions to total energy (kcal/mol):
Valence energy (diag. terms) : 61.509
Bond : 39.031
Angle : 22.479
Torsion : 0.000
Inversion : 0.000
Valence energy (cross terms) : 0.000
Stretch-Stretch : 0.000
Stretch-Bend-Stretch : 0.000
Stretch-Torsion-Stretch : 0.000
Separated-Stretch-Stretch : 0.000
Torsion-Stretch : 0.000
Bend-Bend : 0.000
Torsion-Bend-Bend : 0.000
Bend-Torsion-Bend : 0.000
Non-bond energy : -424.717
van der Waals : 98.043
Electrostatic : -522.759
rms force : 2.767E+002 kcal/mol/A
max force : 3.203E+002 kcal/mol/A
rms stress : 1.496E+002 GPa
max stress : 2.375E+002 GPa
Cell parameters: a: 3.585000 A b: 3.585000 A c: 4.895000 A
alpha: 90.000 deg beta: 90.000 deg gamma: 120.000 deg
---- Final structure ----
Total enthalpy : -581.268626 kcal/mol
External pressure term : 0.000000 kcal/mol
Total energy : -581.268626 kcal/mol
Contributions to total energy (kcal/mol):
Valence energy (diag. terms) : 36.815
Bond : 0.285
Angle : 36.529
Torsion : 0.000
Inversion : 0.000
Valence energy (cross terms) : 0.000
Stretch-Stretch : 0.000
Stretch-Bend-Stretch : 0.000
Stretch-Torsion-Stretch : 0.000
Separated-Stretch-Stretch : 0.000
Torsion-Stretch : 0.000
Bend-Bend : 0.000
Torsion-Bend-Bend : 0.000
Bend-Torsion-Bend : 0.000
Non-bond energy : -618.083
van der Waals : 37.914
Electrostatic : -655.998
rms force : 8.028E-002 kcal/mol/A
max force : 8.341E-002 kcal/mol/A
rms stress : 1.454E-002 GPa
max stress : 2.392E-002 GPa
Cell parameters: a: 3.766875 A b: 3.766875 A c: 5.045237 A
alpha: 90.000 deg beta: 90.000 deg gamma: 120.000 deg
Task terminated : Tue Jul 15 12:59:34 2014
Total CPU time used by Forcite: 1 seconds (1.5s)
Termination status : Normal
Micheal,
When I used COMPASS with auto force field type and force field charges, I am getting following values,
-- Energy parameters ----
Forcefield : COMPASSII (Version 1.1)
Charges : Forcefield assigned
Electrostatic terms:
Summation method : Ewald
Accuracy : 0.001 kcal/mol
Buffer width : 0.5 A
van der Waals terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 12.5 A
Spline width : 1 A
Long range correction : YES
Buffer width : 0.5 A
Energy contributors with missing parameters:
Bond Stretch : (ca2o o)
Angle Bend : (o ca2o o)
Torsion : (o ca2o o ca2o), (o ca2o o h1o)
Energy contributors using automatic parameters:
Angle Bend : (ca2o o ca2o), (ca2o o h1o)
---- Initial structure ----
Total enthalpy : -920.250333 kcal/mol
External pressure term : 0.000000 kcal/mol
Total energy : -920.250333 kcal/mol
Contributions to total energy (kcal/mol):
Valence energy (diag. terms) : 23.329
Bond : 0.212
Angle : 23.117
Torsion : 0.000
Inversion : 0.000
Valence energy (cross terms) : 0.000
Stretch-Stretch : 0.000
Stretch-Bend-Stretch : 0.000
Stretch-Torsion-Stretch : 0.000
Separated-Stretch-Stretch : 0.000
Torsion-Stretch : 0.000
Bend-Bend : 0.000
Torsion-Bend-Bend : 0.000
Bend-Torsion-Bend : 0.000
Non-bond energy : -943.579
van der Waals : 94.493
Long range correction : -0.485
Electrostatic : -1037.587
rms force : 2.245E+001 kcal/mol/A
max force : 2.705E+001 kcal/mol/A
rms stress : 9.405E+000 GPa
max stress : 1.721E+001 GPa
Cell parameters: a: 3.591800 A b: 3.591800 A c: 4.906300 A
alpha: 90.000 deg beta: 90.000 deg gamma: 120.000 deg
---- Final structure ----
Total enthalpy : -942.475145 kcal/mol
External pressure term : 0.000000 kcal/mol
Total energy : -942.475145 kcal/mol
Contributions to total energy (kcal/mol):
Valence energy (diag. terms) : 6.812
Bond : 0.842
Angle : 5.969
Torsion : 0.000
Inversion : 0.000
Valence energy (cross terms) : 0.000
Stretch-Stretch : 0.000
Stretch-Bend-Stretch : 0.000
Stretch-Torsion-Stretch : 0.000
Separated-Stretch-Stretch : 0.000
Torsion-Stretch : 0.000
Bend-Bend : 0.000
Torsion-Bend-Bend : 0.000
Bend-Torsion-Bend : 0.000
Non-bond energy : -949.287
van der Waals : 72.779
Long range correction : -0.617
Electrostatic : -1021.449
rms force : 9.379E-003 kcal/mol/A
max force : 1.173E-002 kcal/mol/A
rms stress : 9.272E-003 GPa
max stress : 1.533E-002 GPa
Cell parameters: a: 3.809476 A b: 3.809476 A c: 3.431986 A
alpha: 90.000 deg beta: 90.000 deg gamma: 120.000 deg
Task terminated : Tue Oct 28 10:36:36 2014
Total CPU time used by Forcite: 1 seconds (0.84s)
Termination status : Normal
Also, Density is changing 2.8 g/cc from 2.2 g/cc
Which force filed parameters do you used when you ran above simulations? Did you use force field assigned charges or other charges ?
Thank you.
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