### Example DISTCON file content Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example of atom-atom harmonic distance constraint potential entries. ```text 367 393 2.27 1.01D3 372 385 2.65 1.02D3 ``` -------------------------------- ### Build standalone dftpb binary Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Manual steps to build and install the standalone dftpb binary. ```bash FC=ifort CC=icc cmake -DCMAKE_INSTALL_PREFIX=$HOME/softwarewales/DFTBP/_build -B _build . ``` ```bash cmake --build $HOME/softwarewales/DFTBP/_build -- -j ``` ```bash cmake --install $HOME/softwarewales/DFTBP/_build ``` -------------------------------- ### Atomgroups File Format Example Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example of an atomgroups file containing two groups, OME and CH2OH. ```text GROUP OME 6 5 4 1.0 0.8 1 2 3 4 GROUP CH2OH 23 25 4 1.0 0.8 26 27 28 29 ``` -------------------------------- ### GLJ Potential Specification Example Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example of specifying a 13-atom cluster with three different species using the GLJ keyword. ```text GLJ 6 4 3 1.0 1.1 1.2 1.2 1.3 1.4 1.0 1.5 1.6 1.7 1.8 1.9 ``` -------------------------------- ### ZSYM File for H2 Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example content for the ZSYM file required when using ORCA with GMIN. ```text H H ``` -------------------------------- ### ORCA Template for H2 DFT Calculation Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example content for the ORCA.template file to perform a DFT calculation for H2. ```text ! B3LYP ENGRAD def2-TZVP ``` -------------------------------- ### MPI job submission for 20 tasks Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node4.html Example sbatch script for running GMIN with 20 MPI tasks. The number of replicas corresponds to the number of MPI tasks, specified in the sbatch script. ```bash #SBATCH -n20 -N1 #SBATCH –tasks-per-node=20 ``` ```bash mpirun -n 20 /sharedscratch/wales/GMIN.gfortran.mpi/GMIN > output ``` -------------------------------- ### Compile GMIN with LAMMPS support Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example cmake command for compiling GMIN with LAMMPS support on the DJWlammps branch. ```bash FC=mpif90 CC=mpicc CXX=mpicxx cmake -DWITH_LAMMPS=1 ~/softwarewales/GMIN/source/ -DCOMPILER_SWITCH=gfortran ``` -------------------------------- ### ORCA Template for Restricted Hartree-Fock Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example ORCA.template for a Restricted Hartree-Fock calculation using 16 MPI processes and disabling dipole moment calculation. ```text ! RHF ENGRAD def2-SVP MiniPrint %PAL NPROCS 16 END %elprop Dipole False end ``` -------------------------------- ### Compile GMIN with LAMMPS support on lammps_mpi branch Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example cmake command for compiling GMIN with LAMMPS support on the lammps_mpi branch. ```bash FC=mpif90 CC=mpicc CXX=mpicxx cmake /softwarewales/GMIN/source -DCOMPILER_SWITCH=gfortran -DWITH_LAMMPS=yes -DWITH_ALIGN=no -DWITH_MYBLAS=yes -DWITH_MYLAPACK=yes ``` -------------------------------- ### Define Multicomponent Sutton-Chen (MSC) Potential Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example of specifying a ternary system AN-k-lBkCl using six consecutive lines for the MSC keyword. ```text _MSC_ | 3 | _nnAA_ | _mmAA_ | _sigAA_ | _scepsAA_ | _sccA_ ---|---|---|---|---|---|--- _MSC_ | | _nnAB_ | _mmAB_ | _sigAB_ | _scepsAB_ | _MSC_ | | _nnAC_ | _nnAC_ | _sigAC_ | _scepsAC_ | _MSC_ | _k_ | _nnBB_ | _nnBB_ | _sigBB_ | _scepsBB_ | _sccB_ _MSC_ | | _nnBC_ | _nnBC_ | _sigBC_ | _scepsBC_ | _MSC_ | _l_ | _nnCC_ | _nnCC_ | _sigCC_ | _scepsCC_ | _sccC_ ``` -------------------------------- ### Side-chain torsion atomgroups file for ARG-GLU dipeptide Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Example atomgroups file for side-chain torsions of an ARG-GLU dipeptide, generated from the input.pdb structure. Each GROUP line defines a torsion (e.g., ARG1CACB) with atom indices and parameters, followed by the list of atoms in that group. ```plaintext GROUP ARG1CACB 3 5 17 0.25 0.25 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 GROUP ARG1CBCG 5 8 14 0.25 0.25 9 10 11 12 13 14 15 16 17 18 19 20 21 22 GROUP GLU2CACB 27 29 8 0.25 0.25 30 31 32 33 34 35 36 37 GROUP GLU2CBCG 29 32 5 0.25 0.25 33 34 35 36 37 ``` -------------------------------- ### Stockmayer rbdata file Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node40.html Example rbdata file for a Stockmayer fluid. It defines two sites with zero coordinates and orientation, and specifies Lennard-Jones (lj) interactions between identical sites and a dipole interaction between the two sites. ```text 2 class 1 site 0.0 0.0 0.0 orient 0.0 0.0 0.0 class 2 site 0.0 0.0 0.0 orient 0.0 0.0 0.0 matrix 1 1 lj 1.0 1.0 1.0 1.0 2 2 dipole 1.0 1.0 ``` -------------------------------- ### Normal LJ rbdata file Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node36.html Example rbdata file for a normal Lennard-Jones (LJ) interaction. The file defines one site at the origin and a matrix with LJ parameters (sigma=1.0, epsilon=1.0, rep=1.0, att=1.0) for the 1-1 interaction. ```plaintext 1 class 1 site 0.0 0.0 0.0 orient 0.0 0.0 0.0 matrix # lj sig eps rep att 1 1 lj 1.0 1.0 1.0 1.0 ``` -------------------------------- ### Configure Intel build for DFTBP Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Load Intel modules and configure the build with the appropriate compiler environment variables. ```bash cmake/3.23.2 idb/latest icc/64/2022/0/1 tbb/64/2022/0/1 oneapi-compiler-rt/64/2022/0/1 mkl/64/2022/0/0 ``` ```bash FC=ifort CC=icc CXX=icc cmake ~/softwarewales/GMIN/source/ -DWITH_DFTBP=yes ``` ```bash make ``` -------------------------------- ### Configure XTBGMIN build with Intel compilers Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Specify the compiler environment variables and run cmake to configure the build with XTBAPI enabled. ```bash FC=ifort CC=icc CXX=icc cmake ~/softwarewales/GMIN/source/ -DWITH_XTBAPI=yes ``` -------------------------------- ### Load Intel modules for XTBGMIN build Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Load the required Intel modules before building XTBGMIN. ```bash cmake/3.23.2 tbb/64/2022/0/1 icc/64/2022/0/1 gcc/12.2.0 idb/latest oneapi-compiler-rt/64/2022/0/1 mkl/64/2022/0/0 ``` -------------------------------- ### Initialize and update DFTBP submodule Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Commands to initialize and update the DFTBP submodule within the softwarewales directory. ```bash git submodule init DFTBP git submodule update ``` -------------------------------- ### Configure GCC build for DFTBP Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Load GCC modules and configure the build specifying the BLAS library path. ```bash gcc/12.2.0, cmake/3.23.2 ``` ```bash cmake ~/softwarewales/GMIN/source/ -DWITH_DFTBP=yes -DWITH_MYBLAS=no -DBLAS_LIBRARIES=/usr/lib64/libopenblas.so.0 ``` -------------------------------- ### Configure parallel tempering basin-hopping with BHPT Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Specifies a parallel tempering basin-hopping run with temperatures and exchange probabilities. Requires the MPI keyword and is typically configured via sbatch scripts. ```bash #SBATCH -n20 -N1 #SBATCH –tasks-per-node=20 ``` -------------------------------- ### Run GMIN with MPI Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Execute GMIN using MPI with 20 processes. ```bash mpirun -n 20 /sharedscratch/wales/GMIN.gfortran.mpi/GMIN > output ``` -------------------------------- ### TIP4P rbdata file Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node39.html Defines a TIP4P water model with four sites: oxygen (O), two hydrogens (H1, H2), and a lone pair (lp). The Lennard-Jones parameters for oxygen are given with a comment noting that eps = 0.25 is needed to cancel the 4.0 in the LJ potential. Coulombic interactions are defined for the hydrogen and lone pair sites with charges 0.52 and -1.04, and k_c = 1389.354848 kJ/mol. ```plaintext 4 # four sites class 1 O 0.0 0.0 0.0 orient 0.0 0.0 0.0 class 2 H1 0.756950327 0.0 -0.5858822760 orient 0.0 0.0 0.0 class 2 H2 -0.756950327 0.0 -0.5858822760 orient 0.0 0.0 0.0 class 3 lp 0.0 0.0 -0.15 orient 0.0 0.0 0.0 matrix # lj sig eps rep att 1 1 lj 1.0 0.25 2510.4d3 2552.24 # need eps = 1/4 to cancel the 4.0 in the LJ potential # rep is kJ angstrom^12 / mol # att is kJ angstrom^6 / mol # coulomb sig k_c q_1 q_2 2 2 coulomb 1.0 1389.354848 0.52 0.52 2 3 coulomb 1.0 1389.354848 0.52 -1.04 3 3 coulomb 1.0 1389.354848 -1.04 -1.04 # k_c is measured in kJ/mol ``` -------------------------------- ### LWOTP rbdata file Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node38.html Defines a three-site water model (LWOTP) with site positions and a single Lennard-Jones interaction matrix. The site coordinates are given in Cartesian units with orientation parameters. The matrix specifies the Lennard-Jones sigma, epsilon, repulsive, and attractive parameters for interactions between site 1 and itself. ```plaintext 3 # three sites class 1 site 0.0 -0.528902226860823 0.0 orient 0.0 0.0 0.0 # 0.0, -2/3 sin 7pi/24, 0.0 class 1 site 0.608761429008721 0.264451113430412 0.0 orient 0.0 0.0 0.0 # cos 7pi/24, 1/3 sin 7pi/24, 0.0 class 1 site -0.608761429008721 0.264451113430412 0.0 orient 0.0 0.0 0.0 # -cos 7pi/24, 1/3 sin 7pi/24, 0.0 matrix # lj sig eps rep att 1 1 lj 1.0 1.0 1.0 1.0 ``` -------------------------------- ### Configure MULTIPOT Potential Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html General format for defining a potential within the multipotconfig file. ```text _POT_ _POTTYPE n scale nparams_ _[params]_ followed by a list of atom indices which will use this potential (the format of the list will depend on the particular potential). ``` -------------------------------- ### Compile GMIN with MPI using cmake Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node4.html Command to compile GMIN with MPI support using cmake and the gfortran compiler switch. ```bash FC=mpifort cmake /̃softwarewales/GMIN/source/ -DCOMPILER_SWITCH=gfortran ``` -------------------------------- ### Compile GMIN with MPI Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Standard CMake command to compile GMIN with MPI support. ```bash FC=mpifort CC=mpicc CCX=mpixx cmake _source_ -DCOMPILER_SWITCH=gfortran -DWITH_MPI=ON -DWITH_AMBER20=ON ``` -------------------------------- ### Define dihedral groups syntax Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Syntax for defining dihedral groups in the dihedralgroups file. ```text GROUP name type at1 at2 at3 at4 _N_ maxrot pselect gat1 gat2 … gatN ``` -------------------------------- ### Backbone dihedral atomgroups file generated by generate_dihedral_atomgroups.py Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Output of running 'python generate_dihedral_atomgroups.py input' on the input.pdb file. It generates GROUP entries for backbone dihedrals such as ARG1psi and GLU2phi, with atom indices and parameters. ```plaintext GROUP ARG1psi 3 23 16 0.25 0.1 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 GROUP GLU2phi 25 27 12 0.25 0.1 28 29 30 31 32 33 34 35 36 37 38 39 ``` -------------------------------- ### Compile GMIN with MPI and CUDA for AMBER Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html CMake command for an MPI build with GPU support, requiring specific module loads for gcc and cuda. ```bash FC=mpif90 CC=mpicc CXX=mpicxx cmake _source_ -DWITH_ALIGN=no -DWITH_AMBER20=yes -DWITH_CUDA=yes -DCOMPILER_SWITCH=gfortran -DWITH_MPI=yes ``` -------------------------------- ### Generate Atomgroups Script Usage Source: https://www-wales.ch.cam.ac.uk/GMIN.doc/node7.html Command to generate an atomgroups file from a PDB file using the provided Python script. ```bash python generate_atomgroups.py input ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.