Hello,
In the GAMESS MAKEFP documentation, it mentions that if a system contains fewer than three atoms, you can add two dummy atoms with dummy coordinates and multipoles, allowing the MAKEFP calculation to proceed successfully. I’m wondering if there’s a similar feature in the libefp module of QChem for modeling monovalent ions, such as Na+ or Cl-, as effective fragments (EFs) alongside water fragments.
I’ve tried using the following input as suggested in the GAMESS manual, but I’m encountering a segmentation fault (core dumped) error. Has anyone else run into this issue or found a solution?
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User input:
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$comment
PDB: so3sq_water-traj1-extract.pdb.10
$end
$molecule
0 1
He 5.0 5.0 5.0
$end
$efp_fragments
na_ion
A01NA1 18.037001 32.077999 17.301001
A02He 5.0 5.0 5.0
A03He 5.0 5.0 5.0
na_ion
A01NA1 11.189000 15.839000 19.089001
A02HeHe 5.0 5.0 5.0
A03HeH 5.0 5.0 5.0
water_u
A01O1 27.062000 17.833000 2.781000
A02H2 27.858000 18.250999 3.111000
A03H3 26.504000 17.740000 3.553000
water_u
A01O1 33.230999 16.292999 11.138000
A02H2 33.622002 16.677999 11.922000
A03H3 33.470001 15.367000 11.180000
water_u
A01O1 34.515999 22.712999 21.739000
A02H2 34.146999 21.872000 21.469000
A03H3 35.313999 22.802999 21.216999
water_u
A01O1 23.830999 35.373001 7.635000
A02H2 23.812000 34.798000 8.401000
A03H3 23.372000 34.881001 6.955000
$end
$rem
JOBTYPE SP
METHOD wb97x-d
BASIS 6-31+G(d)
BASIS2 STO-3G
!PURECART 2222
!tddft parameters
!CIS_N_ROOTS 10
!CIS_SINGLETS true
!CIS_TRIPLETS false
!RPA true
!efp parameters
EFP true
EFP_FRAGMENTS_ONLY true
EFP_COORD_XYZ true
EFP_DIRECT_POLARIZATION_DRIVER true
EFP_EXREP false
EFP_DISP true
EFP_ELEC_DAMP 1 !Overlap-based damping and 2 for Screen-based damping
!EFP_DISP_DAMP 1 !TT damping and 2 for Overlap-based damping
!EFP_POL_DAMP 1
!scf
THRESH 14
S2THRESH 16
MAX_SCF_CYCLES 120
SCF_CONVERGENCE 8
!SCF_GUESS read
MEM_TOTAL 16000 ! Specify memory in megabytes (16 GB)
$end
Output does not correctly identify Na+ cations.
GEOMETRY OF EFP SUBSYSTEM
A01NA1 -nan -nan -nan
A01NA1 -nan -nan -nan
A01O1 27.06200 17.83300 2.78100
A02H2 27.84330 18.24328 3.10491
A03H3 26.49143 17.72799 3.52066
A01O1 33.23100 16.29300 11.13800
A02H2 33.61509 16.67119 11.90814
A03H3 33.45091 15.37917 11.15338
A01O1 34.51600 22.71300 21.73900
A02H2 34.15364 21.88713 21.47386
A03H3 35.30449 22.82894 21.24049
A01O1 23.83100 35.37300 7.63500
A02H2 23.81236 34.80877 8.38665
A03H3 23.38471 34.91325 6.94715
Following is how the efp parameter file looks like for Na fragment.
$na_ion
Sodium, All:6-311++G(3df,2p) 5-test_BOYS_CTVVO-FALSE
COORDINATES (BOHR)
A01NA1 0.0000000000 0.0000000000 0.0000000000 22.9898000 11.0
A02He 0.0000000000 0.0000000000 0.0000000000 0.00000000 0.0
A02He 0.0000000000 0.0000000000 0.0000000000 0.00000000 0.0
STOP
MONOPOLES
A01NA1 -10.0000000000 11.00000
A02He 0.0000000000 0.000000
A02He 0.0000000000 0.000000
STOP