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