I am trying to perform a TDDFT calculation for a dye - water system. Previous attempts for TDDFT of dye was successful. Because of that I have been using a similar input for the current calculation. Only difference is surrounding water box is modeled using electrostatic embedding (JANUS). I have attached the input and output file of this. I tried setting different MEM_TOTAL values assuming a memory issue while also completely removing the MEM_TOTAL flag. Still the calculation crashes at the very beginning with “segmentation fault: core dumped” error. I appreciate any thoughts as to validity of the input and what I could try to address the error.
output:
6376 H 7.8110000000 35.9350000000 25.2140000000
----------------------------------------------------------------
Nuclear Repulsion Energy = 0.00000000 hartrees
There are 10739 alpha and 10739 beta electrons
Total QAlloc Memory Limit 2000 MB
Mega-Array Size 188 MB
MEM_STATIC part 192 MB
**** Step 1: MM energy contributions ****
AMBER99 force field loaded.
Time req'd to get MM system information: 693.8 s (CPU) 694.2 s (wall)
Please provide the input.
My input exceeds the body limit for messages. What is the recommended way to share the input file?
Then please find a smaller example that fails in the same way. This is always the recommended procedure when reporting bugs: minimal example.
FYI, if all you want to do are single point TDDFT calculations with point-charge embedding, it’s probably easier to use the $external_charges section rather than the Janus QM/MM, which is under-developed. TDDFT with external charges works for very large MM regions (have done it myself), but it’s for single-point calculations only.
I tried to do the same calculation with removing majority water molecules. Now the calculation proceeds however I am getting a different error.
**** Step 1: MM energy contributions ****
AMBER99 force field loaded.
Time req'd to get MM system information: 0.0 s (CPU) 0.0 s (wall)
Unknown angle bending parameter for 21-42-30
Q-Chem fatal error occurred in module forceman/angle_params_AMBER.C, line 230:
Undefined angle parameter.
$comment
PDB: so3sq_water-traj1-extract.pdb.1
Janus YingYang embedding. MM: AMBER99 (water+ions). QM: wB97x-D/6-31+G* (SO3SQ).
20 excited states. Assumed MM interactions same for excited and ground states.
Gaussian-blurred MM charges, width: 1.5 Ã….
$end
$molecule
0 1
C 25.221000 19.485000 17.045000 0
O 26.375000 19.525000 17.519000 0
C 24.792000 19.399000 15.677000 0
C 23.566000 18.692000 16.074000 0
O 22.802000 18.078000 15.449000 0
C 24.103000 18.618000 17.410000 0
C 24.694000 17.635000 22.442000 0
H 24.874000 17.623000 23.513000 0
C 25.145000 18.746000 21.775000 0
H 25.511000 19.564000 22.389000 0
C 24.923000 18.750000 20.369000 0
H 25.148000 19.619000 19.752000 0
N 24.397000 17.639000 19.712000 0
C 23.850000 16.606000 20.396000 0
C 24.018000 16.526000 21.782000 0
H 23.599000 15.666000 22.295000 0
C 23.735000 17.691000 18.504000 0
C 22.760000 16.734000 18.423000 0
C 22.828000 15.982000 19.587000 0
C 21.801000 14.906000 20.019000 0
H 20.758000 15.243000 20.023000 0
H 22.063000 14.494000 21.000000 0
H 21.824000 14.094000 19.283000 0
C 21.523000 17.193000 18.099000 0
C 24.867000 17.971000 10.472000 0
H 24.756000 17.414000 9.546000 0
C 23.805000 17.892000 11.446000 0
H 22.838000 17.613000 11.037000 0
C 23.841000 18.561000 12.672000 0
H 22.918000 18.789000 13.203000 0
N 25.085000 19.047000 13.100000 0
C 26.179000 18.893000 12.241000 0
C 26.104000 18.527000 10.887000 0
H 26.928000 18.767000 10.221000 0
C 25.526000 19.481000 14.402000 0
C 26.869000 19.779000 14.169000 0
C 27.218000 19.442000 12.919000 0
C 28.510000 19.938000 12.180000 0
H 28.416000 20.152000 11.109000 0
H 29.288000 19.172000 12.282000 0
H 28.876000 20.866000 12.633000 0
C 21.082000 18.543000 18.417000 0
H 21.758000 19.167000 18.994000 0
C 19.789000 18.999000 18.209000 0
H 19.550000 20.029000 18.456000 0
C 18.834000 18.167000 17.649000 0
C 19.230000 16.839000 17.288000 0
H 18.572000 16.071000 16.892000 0
C 20.537000 16.392000 17.536000 0
H 20.791000 15.374000 17.256000 0
O 17.555000 18.490000 17.473000 0
C 17.170000 19.838000 17.494000 0
H 17.018000 20.214000 18.513000 0
H 17.966000 20.362000 16.950000 0
C 15.914000 20.116000 16.715000 0
H 15.566000 21.132000 16.936000 0
H 15.122000 19.457000 17.088000 0
C 16.132000 19.830000 15.198000 0
H 16.936000 20.497000 14.867000 0
H 16.480000 18.800000 15.063000 0
C 14.819000 19.948000 14.409000 0
H 14.444000 20.979000 14.436000 0
H 14.124000 19.220000 14.847000 0
S 15.031000 19.386000 12.687000 0
O 13.833000 19.936000 11.992000 0
O 14.982000 17.947000 12.814000 0
O 16.314000 19.941000 12.232000 0
C 27.637000 20.719000 15.050000 0
C 26.974000 21.795000 15.668000 0
H 25.976000 22.068000 15.337000 0
C 27.804000 22.706000 16.476000 0
H 27.298000 23.539000 16.955000 0
C 29.192000 22.363000 16.684000 0
C 29.784000 21.187000 16.160000 0
H 30.818000 20.904000 16.335000 0
C 28.931000 20.316000 15.340000 0
H 29.306000 19.430000 14.836000 0
O 29.989000 23.160000 17.487000 0
C 29.421000 24.310000 18.216000 0
H 28.644000 24.034000 18.941000 0
H 28.987000 24.979000 17.463000 0
C 30.569000 24.915000 18.902000 0
H 30.963000 24.095000 19.513000 0
H 31.258000 25.215000 18.105000 0
C 30.202000 26.124000 19.783000 0
H 29.430000 25.929000 20.536000 0
H 29.743000 26.947000 19.225000 0
C 31.379000 26.730000 20.606000 0
H 31.757000 25.987000 21.319000 0
H 32.093000 27.111000 19.865000 0
S 30.843000 28.221000 21.523000 0
O 29.648000 27.778000 22.269000 0
O 32.015000 28.637000 22.324000 0
O 30.629000 29.174000 20.441000 0
Na 0.266000 37.718000 4.366000 2004
Na 37.413000 34.022000 20.981000 2004
Na 6.051000 17.981000 29.361000 2004
Na 3.264000 28.929000 8.808000 2004
Na 36.702000 15.856000 2.857000 2004
Na 25.861000 4.470000 9.358000 2004
Na 46.038000 26.963000 27.611000 2004
Cl 34.634000 21.974000 19.209000 2012
Cl 22.968000 32.969000 5.942000 2012
Cl 14.182000 1.803000 3.000000 2012
Cl 37.232000 19.132000 7.483000 2012
Cl 41.258000 26.765000 25.884000 2012
O 23.239000 6.039000 14.345000 2001
H 23.404000 6.884000 13.927000 2002
H 22.327000 5.840000 14.132000 2002
O 43.896000 32.519000 26.392000 2001
H 43.065000 32.268000 25.990000 2002
H 43.927000 32.022000 27.209000 2002
O 5.716000 30.882000 33.006000 2001
H 5.180000 31.606000 33.329000 2002
H 6.618000 31.176000 33.134000 2002
$end
$rem
JOBTYPE SP
METHOD wB97x-D
BASIS 6-31+G*
QM_MM_INTERFACE janus
FORCE_FIELD amber99
GAUSSIAN_BLUR true
GAUSS_BLUR_WIDTH 15000
MODEL_SYSTEM_CHARGE -2
MODEL_SYSTEM_MULT 1
CIS_N_ROOTS 20
CIS_SINGLETS true
CIS_TRIPLETS false
RPA true
MAXSCF 5000
MEM_TOTAL 16000
$end
$qm_atoms
1:94
$end
I will also try to apply $external_charges approach for the MM region. The segmentation fault most probably resulted due to the large solvent box size I used (over 6000 atoms).
It means that Q-Chem’s version of that force field parameter file doesn’t contain the bond-angle parameter that you want, which you would need to add. If you’re just looking to add charges, use $external_charges. If you’re really looking to do QM/MM, I suggest you look into one of the MM codes that can interface with Q-Chem.
Thanks @jherbert for your valuable advice. I will move in to using $external_charges for this purpose.