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Messages - pbs13

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I am computing N2 adsorption isotherms in UiO-66 using two different methods of specifying the UiO-66 framework.

The first approach is to use a CIF file for the primitive cell, which is triclinic and contains 114 atoms. I used the UnitCells 3 3 3 command to create a supercell with 27 primitive cells (total of 3078 atoms).

The second approach used a CIF file containing a large cubic supercell containing 3648 atoms. This simulation used UnitCells 1 1 1.

The second simulation took about 10x longer to run, even though the size of the simulation cell was not that different. Why is there such a big difference in the simulation times for these two systems? Is it less efficient to have a large CIF file and use a single unit cell compared with having a small CIF file and replicate the cell?
 

2
Hello Professor,

I am trying to run NPT simulation for isopropanol molecule. The AUA4 isopropanol pseudoatoms.def looks like -
#number of pseudo atoms
4
#type   print   as   scat   oxidation   mass   charge   polarization   B-factor   radius   connectivity   anisotropic   anisotropic-type   tinker-type
CH   yes   CH   0   0      13.019   0.265   0      1.0      1.00   3      0.646      absolute      0
O_IPA   yes   O   0   0      15.9994   -0.70   0      1.0      0.66   2      0.010      absolute      0
H_IPA   yes   H   0   0      1.008   0.435   0      1.0      0.31   1      0      absolute      0
CH3   yes   CH3   0   0      15.0345   0.0   0      1.0      1.00   1      0.216      absolute      0

After I run NPT simulation, I get an error -
ERROR: undefined anisotropic atom with connecvity: 3, in routine 'CalculateAnisotropicTrialPositions' (cbmc.c)

The isopropanol.def file looks like -
#critical constants: temp [T], pressure [Pa], acentric factor [-]
508.3
4760000.0
0.665
#number of atoms
5
#number of groups
1
#molecule-group
flexible
#number of atoms
5
#atomic positions
0 CH
1 O_IPA
2 H_IPA
3 CH3
4 CH3
#chiralCenters bond bondDipoles   bend urayBradley invBend torsion torsionIMP bond/bond stretch/bend bend/bend stretch/torsion bend/torsion intraVDW intraCoulomb
        0     4         0      4           0       0       2     0        0            0      0         0      0        0            0
#bond stretch: atoms, n1-n2, type, parameters
0 1 FIXED_BOND 1.430
0 3 FIXED_BOND 1.535
0 4 FIXED_BOND 1.535
1 2 FIXED_BOND 0.945
#bond bending: atom n1-n2-n3, type parameters
3 0 4 HARMONIC_COSINE_BEND 72700 112.0
3 0 1 HARMONIC_COSINE_BEND 59800 109.47
4 0 1 HARMONIC_COSINE_BEND 59800 109.47
0 1 2 HARMONIC_COSINE_BEND 61000 108.5
#bond torsion n1-n2-n3-n4 type parameters
3 0 1 2 TRAPPE_DIHEDRAL 215.96 197.33 31.46 -173.92
4 0 1 2 TRAPPE_DIHEDRAL 215.96 197.33 31.46 -173.92
#number of config moves
0

The force_field_mixingrules.def file is -
#general rule for shifted or truncated cutoff
truncated
#general rule for cutoff tail correction
yes
#number of defined interactions
4
#type interaction using UFF
CH    LENNARD_JONES 50.980   3.363
O_IPA      LENNARD_JONES 125.010   3.081
H_IPA      LENNARD_JONES 0.000   0.000
CH3  LENNARD_JONES 120.1500   3.607
#general mixing rule for LJ
Lorentz-Berthelot

Anticipating an early response.

Thank you,
Best,
Priyanka



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