Project Report:

    Introduction 
    Water Potential
    MD simulations 
    Results 
    Conclusions
    References

Slides

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Team 2 

Xiaohai Li
Vamsi Akkineni
Jianwei Wang 

Fall, 2002 

 MD Studies of LDL and HDL Phases of Supercooled Water 

Xiaohai Li, Vamsi Akkineni, Jianwei Wang


MD simulations:
Ensemble: NVT
Number of water molecules: 125
Use periodic boundry conditions
Time step: 0.001ps
Equilibration: 500ps
Collect data: 1000ps
Initial configuration: Random distributed water molecules in a cubic box with appropriate density, then minimize the system energy.
Ewald summation used for long range Coulombic forces.
Cutoff used for Lennard-Jones interactions (7Å)
 
Density: 0.95g/cm3 , (15.789216 Å)3 cubic, 
16 prcessors on Origin 2000, 16 Hours
 
 
 
 
 
 
 
 
 
 

 

 
Density: 1.20g/cm3 , (15.789216 Å)3 cubic, 
16 prcessors on Origin 2000, 16 Hours
 
 
 
 
 
 
 

 

SPC Force for CERIUS2:

VERSION
CERIUS2     1
END
#
HEADER
END
#
PREFERENCES
 BONDS                                 T
 ANGLES                                T
 COULOMB                               T
 INVERSIONS                            F
 TORSIONS                              F
 UREY_BRADLEY                          F
 STRETCH_STRETCH                       F
 SEPARATED_STRETCH_STRETCH             F
 STRETCH_BEND_STRETCH                  F
 BEND_BEND                             F
 TORSION_STRETCH                       F
 TORSION_BEND_BEND                     F
 BEND_TORSION_BEND                     F
 STRETCH_TORSION_STRETCH               F
 HYDROGEN_BONDS                        F
 DIAGONAL_VAN_DER_WAALS                T
 OFF_DIAGONAL_VAN_DER_WAALS            T
 IGNORE_UNDEFINED_TERMS                F
 NON-BONDED_3-BODY                     F
 SHRINK_CH_BONDS                       F
 SHRINK_CH_H_ATOM                      H__C
 SHRINK_CH_FACTOR                         0.91500
 SINGLE_TORSION                        F
 SCALE_TORSIONS_ABOUT_COMMON_BOND      F
 SCALE_BY_N_DEFINED_TORSIONS           T
 EXOCYCLIC_TORSIONS_SCALE_FACTOR          0.40000
 SINGLE_INVERSION                      F
 H-BOND_METHOD                         SPLINE
 H-BOND_LIST                           T
 H-BOND_DIRECT_RCUT                       4.00000
 H-BOND_SPLINE_DISTANCE_ON                4.00000
 H-BOND_SPLINE_DISTANCE_OFF               4.50000
 H-BOND_SPLINE_ANGLE_ON                  65.00000
 H-BOND_SPLINE_ANGLE_OFF                 75.00000
 H-BOND_LIST_DISTANCE_OFF                 6.50000
 H-BOND_LIST_ANGLE_OFF                   90.00000
 NB_NEIGHBOUR_SEARCH_METHOD            LIST                         
 NON_BOND_BUFFER_DISTANCE                 2.00000
 H-BOND_BUFFER_DISTANCE                   2.00000
 COU_DIELETRIC_CONSTANT                     1.00000000000000000     
 COU_INTER_CUT_OFF                        8.00000
 COU_SPLINE_OFF                           8.50000
 COU_SPLINE_ON                            8.00000
 EWALD_SUM_COU_ACCURACY                   0.00100
 EWALD_SUM_COU_ETA                        3.37300
 EWALD_SUM_COU_KCUT                       0.38800
 EWALD_SUM_COU_RCUT                      11.24000
 EWALD_SUM_COU_OPTIMIZE                SMART                        
 COU_EXCLUDE_1-2                       T
 COU_EXCLUDE_1-3                       T
 COU_EXCLUDE_1-4                       F
 COU_1-4_SCALE_FACTOR                     1.00000
 COU_METHOD                            EWALD                        
 COU_DIRECT_CUT-OFF                       8.00000
 VDW_COMBINATION_RULE                  ARITHMETIC                   
 VDW_INTER_CUT_OFF                        8.00000
 VDW_EXCLUDE_1-2                       T
 VDW_EXCLUDE_1-3                       T
 VDW_EXCLUDE_1-4                       F
 VDW_1-4_SCALE_FACTOR                     1.00000
 VDW_METHOD                            SPLINE                       
 VDW_SPLINE_ON                            8.00000
 VDW_SPLINE_OFF                           8.50000
 EWALD_SUM_VDW_OPTIMIZE                SMART                        
 EWALD_SUM_VDW_ACCURACY                   0.00100
 EWALD_SUM_VDW_ETA                        1.98000
 EWALD_SUM_VDW_KCUT                       0.56000
 EWALD_SUM_VDW_RCUT                       5.50000
 EWALD_SUM_VDW_REP_CUT                    6.40000
 FAST_EWALD_SUM_RATIO                    10.00000
 SLOW_EWALD_SUM_RATIO                     5.00000
 MINIMUM_IMAGE                         F
 ASSIGN_MASS                           T
 ASSIGN_CHARGE                         T
 ASSIGN_HYBRIDIZATION                  F
 ASSIGN_VALBOND_CENTER                 F
 ATOM_TYPE                             F
 ATOM_TYPE_ALL                         T
 CALCULATE_BOND_ORDER                  F
END
#
ATOMTYPES
 h*         H       1.00790  0.4100   1   0   0
 o*         O      15.99940 -0.8200   3   0   0
END
#
DIAGONAL_VDW
 h*          IGNORE        4.577499866485596   
 o*          LJ_6_12       3.553200006484985       0.1553999930620193      
END
#
ATOM_TYPING_RULES
END
#
#
OFF_DIAGONAL_VDW
END
#
BOND_STRETCH
 o*       h*          HARMONIC    1108.2697    1.0000                        
END
#
ANGLE_BEND
 h*       o*       h*          THETA_HARM    91.5392  109.4700                            
END
#
TORSIONS
END
#
COULOMBIC
 X        X           CONST-EPS
END