Theoretical and Structural Chemistry Group of Anápolis
Prof. Dr. Ademir Camargo
You also can get a copy of the source code directly from GitHub:
>> git clone https://github.com/AdemirCamargo57/gqteaMD.git
Installing gqteaMD-0.3.1.whl on Linux
>> sudo dnf install python3.12
>> mkdir gqteaMD
>> cd gqteaMD
>> python3.12 -m venv venv
>> cd venv
>> source ./bin/activate
>> python3.12 -m pip install --upgrade pip
>> python3.12 -m pip install numpy cclib
Download gqteamd-0.3.1-none-any.tgz
>> unzip gqteaMD-0.3.1-py3-none-any.tgz
>> python -m pip install gqteaMD-0.3.1-py3-none-any.whl
>> /home/username/gqteaMD/bin/gqteaMD --help
usage: gqteaMD [-h] {run} ...
positional arguments:
{run}
Run a molecular dynamics simulation
options:
-h, --help show this help message and exit
This message shows that the program was installed correctly. To run a molecular dynamics calculation, you need an XYZ file format with the atomic coordinates and <tomlFileName>.toml. If you are going to use a drive force from Gaussian or xTB Grimme, you need to install it and include the path in the .toml file. To run, type:
>> /home/<username>/gqteaMD/venv/bin/gqteaMD run ./<filename>.toml
The following <tomlFileName>.toml input file was created using the gqteaWingToga program available at https://www.ademircamargo.com/projects
# gqteaMD input generated by gqteaWinToga
[input]
xyz = "water_box.xyz"
[cell]
a = 13.0
b = 13.0
c = 13.0
[dynamics]
timestep_fs = 0.3
steps = 1000
[force_provider]
type = "xtb"
command = "/home/ajc/xtb-dist/bin/xtb"
method = "GFN2-xTB"
charge = 0.0
multiplicity = 1
accuracy = 1.0
electronic_temperature = 300.0
max_iterations = 250
omp_num_threads = 4
solvent = "none"
cache_api = true
use_unwrapped_positions = true
[output]
trajectory = "TRAJEC.xyz"
log = "water_box_gqteaMD.log"
log_interval = 1
[restart]
path = "RESTART"
interval = 5
resume_from_RESTART = true
resume_from_GEOMETRY = false