Talk:Mod:Hunt Research Group/ChemShell files
opt.chm files
An example of an opt.hm file can be seen below.
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 7 22 45 69 82 84 102 137 138 139 140 }\
qm_theory=gaussian : { nproc=7 maxcyc=200 scfconv=5 basisspec={ { 3-21g { N* C* } } { lanl2dz L* } } ecpspec={ { null { N* C* } } { lanl2dz L* } } g98_mem=35000000 charge=-1 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
use_pairlist=no \
mxexcl=300 \
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 } } } \
active_atoms = { 1 7 9 10 11 13 18 20 22 25 27 29 31 32 35 36 43 44 45 48 51 52 58 62 64 65 69 72 74 76 82 83 84 88 94 98 100 101 102 103 105 106 108 109 112 114 115 117 118 120 124 128 129 132 133 134 137 138 139 140 }\
list_option = full \
maxcycle = 300 \
dump = 1 \
result = cluster_opt.pun
It is IMPORTANT that in the "basis spec" section the basis set for non pseudo-potential atoms goes first, followed by the information for the pseudo-potential atoms. The same applies for the "ecpspec" keyword.
Each of the 'keywords' are explains in the following table.
| Keyword | To Specify |
|---|---|
| dl_find | optimisation library, recommended by ChemShell |
| coords= cluster.pun | initial coordinates of system, found in cluster.pun |
| theory=hybrid: | sets up a QM/MM model based on one QM and one MM region |
| cutoff | cutoff for QM/MM electrostatic interactions, we assume this is angstroms |
| qm_region | list of atoms in QM part, list the atoms from *.pun file |
| qm_theory=gaussian | module used for QM energy and forces |
| mm_theory=dl_poly | module used for MM energy and forces |
| mxexcl | Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom?? |
| atom types | atom type settings |
| groups | specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff |
| Active atoms | Atoms that move, i think in the MM region |
| list_option | how much output to generate |
| maxcycle | maximum number of optimisation cycles |
| dump | writes info every dump steps |
| restart | restarts from dump file |
| result | optimised coordinates |
I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about
general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html
Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum
Keyword dispersion_correction=gd3bj
ff.dat
Contains the MM parameters. It is necessary to the have the parameters as C6 and C12 and in kCal
An example ff.dat file is shown below for an La NaCl system.
vdw NA NA 87.5812212 14750.8882 vdw NA CL 522.364248 593182.84 vdw CL CL 3106.1365 24120183.2 vdw LA CL 1471.76193 6991022.6 vdw LA NA 284.384407 228931.111 vdw LA LA 667.42017 1856038.3 charge NA 1.000 charge CL -1.000 charge LA 3.000
To generate the parameters for the ff.dat file some work needs to be completed!
I took the E and sigma values from my MD simulation using the LJ potential and completed a couple of transformations to ensure the correct values were being used. First I had to change E and sigma to C6 and C12 values.
To generate the C6 value needed the calculation needed is 4*E*sigma^6 To generate the C12 value needed the calculation needed is 4*E*sigma^12
These values are in kJ but we need kCal here, so each value is then multiplied by 0.239006 to get values in kCal.
To ensure this process was correct I took Asiwaryas FIELD file from the MD and completed the above calculations. I then compared the values I obtained and the values in the ff.dat she was using and found no difference.
cluster.pun
cluster_x.pun contains the coordinates, charges and connectivity of the cluster.
Example file
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.
cluster_1.chm
generated by MolCluster and transferred to HPC. cluster_1.chm is used to generate the custer.pun file.
cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.
The first line of this file will contain the following.
c_create coords=cluster.pun
This line tells chemshell to generate a file called cluster.pun using the coordinate in the file