Plugin on the Commandline¶
Before attempting to use the features here, you need to have completed the steps in Installation and started the verdi daemon as described in Start/Stop AiiDA.
With our plugin, we are aiming for as simple a transition to using these tools as is possible, so the design philosophy we have chosen is to attempt to mimmick as much as is possible the functionality of native gromacs CLI tools. We currently support the following set of commandline tools and their full feature set. We also have implemented a genericMD CLI interface to provide support for features that we currently do not have, or newly released in the gromacs application.
It is through this powerful interface that you will be able to build powerful workflows or use data provenance capturing tools in this plugin in your existing ways of working without cultural change in the way that you work!
The following utilities are available and have the following features.
gmx_editconf¶
Our plugin introduces a new CLI program utility that supports all of the commandline functionality of the original editconf executable listed here
If the original command is used like this:
gmx editconf -f 1AKI_forcefield.gro -center 0 -d 1.0 -bt cubic -o 1AKI_newbox.gro
Then in our plugin, you would use it like this:
gmx_editconf -f 1AKI_forcefield.gro -center 0 -d 1.0 -bt cubic -o 1AKI_newbox.gro
This utility has extra functionality, such as if you run the command with –help then it will print out comprehensive documentation for usage. There are also two commandline flags for controlling AiiDA parameters that are not native to gromacs. These are:
- --code
This allows you to specify different gromacs installs, either local or remote or different versions
- --description
This allows you to specify a short description of the command operation for metadata, you should provide this in quotes on the commandline.
An example specifying gromacs on the local PC is below:
gmx_editconf --code gmx@localhost -f 1AKI_forcefield.gro -center 0 -d 1.0 -bt cubic -o 1AKI_newbox.gro
gmx_genion¶
Our plugin introduces a new CLI program utility that supports all of the commandline functionality of the original editconf executable listed here
If the original command is used like this:
gmx genion -s 1AKI_ions.tpr -p 1AKI_topology.top -pname NA -nname CL -neutral true -o 1AKI_solvated_ions.gro
Then in our plugin, you would use it like this:
gmx_genion -s 1AKI_ions.tpr -p 1AKI_topology.top -pname NA -nname CL -neutral true -o 1AKI_solvated_ions.gro
This utility has extra functionality, such as if you run the command with –help then it will print out comprehensive documentation for usage. There are also two commandline flags for controlling AiiDA parameters that are not native to gromacs. These are:
- --code
This allows you to specify different gromacs installs, either local or remote or different versions
- --description
This allows you to specify a short description of the command operation for metadata, you should provide this in quotes on the commandline.
An example specifying gromacs on the local PC is below:
gmx_genion --code gmx@localhost -s 1AKI_ions.tpr -p 1AKI_topology.top -pname NA -nname CL -neutral true -o 1AKI_solvated_ions.gro
gmx_grompp¶
Our plugin introduces a new CLI program utility that supports all of the commandline functionality of the original editconf executable listed here
If the original command is used like this:
gmx grompp -f ions.mdp -c 1AKI_solvated.gro -p 1AKI_topology.top -o 1AKI_ions.tpr
Then in our plugin, you would use it like this:
gmx_grompp -f ions.mdp -c 1AKI_solvated.gro -p 1AKI_topology.top -o 1AKI_ions.tpr
This utility has extra functionality, such as if you run the command with –help then it will print out comprehensive documentation for usage. There are also two commandline flags for controlling AiiDA parameters that are not native to gromacs. These are:
- --code
This allows you to specify different gromacs installs, either local or remote or different versions
- --description
This allows you to specify a short description of the command operation for metadata, you should provide this in quotes on the commandline.
An example specifying gromacs on the local PC is below:
gmx_grompp --code gmx@localhost -f ions.mdp -c 1AKI_solvated.gro -p 1AKI_topology.top -o 1AKI_ions.tpr
gmx_mdrun¶
Our plugin introduces a new CLI program utility that supports all of the commandline functionality of the original editconf executable listed here
If the original command is used like this:
gmx mdrun -s 1AKI_em.tpr -c 1AKI_minimised.gro -e 1AKI_minimised.edr -g 1AKI_minimised.log -o 1AKI_minimised.trr
Then in our plugin, you would use it like this:
gmx_mdrun -s 1AKI_em.tpr -c 1AKI_minimised.gro -e 1AKI_minimised.edr -g 1AKI_minimised.log -o 1AKI_minimised.trr
This utility has extra functionality, such as if you run the command with –help then it will print out comprehensive documentation for usage. There are also two commandline flags for controlling AiiDA parameters that are not native to gromacs. These are:
- --code
This allows you to specify different gromacs installs, either local or remote or different versions
- --description
This allows you to specify a short description of the command operation for metadata, you should provide this in quotes on the commandline.
An example specifying gromacs on the local PC is below:
gmx_mdrun --code gmx@localhost -s 1AKI_em.tpr -c 1AKI_minimised.gro -e 1AKI_minimised.edr -g 1AKI_minimised.log -o 1AKI_minimised.trr
gmx_pdb2gmx¶
Our plugin introduces a new CLI program utility that supports all of the commandline functionality of the original editconf executable listed here
If the original command is used like this:
gmx pdb2gmx -f 1AKI_clean.pdb -ff oplsaa -water spce -o 1AKI_forcefield.gro -p 1AKI_topology.top -i 1AKI_restraints.itp
Then in our plugin, you would use it like this:
gmx_pdb2gmx -f 1AKI_clean.pdb -ff oplsaa -water spce -o 1AKI_forcefield.gro -p 1AKI_topology.top -i 1AKI_restraints.itp
This utility has extra functionality, such as if you run the command with –help then it will print out comprehensive documentation for usage. There are also two commandline flags for controlling AiiDA parameters that are not native to gromacs. These are:
- --code
This allows you to specify different gromacs installs, either local or remote or different versions
- --description
This allows you to specify a short description of the command operation for metadata, you should provide this in quotes on the commandline.
An example specifying gromacs on the local PC is below:
gmx_pdb2gmx --code gmx@localhost -f 1AKI_clean.pdb -ff oplsaa -water spce -o 1AKI_forcefield.gro -p 1AKI_topology.top -i 1AKI_restraints.itp
gmx_solvate¶
Our plugin introduces a new CLI program utility that supports all of the commandline functionality of the original editconf executable listed here
If the original command is used like this:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -p 1AKI_topology.top -o 1AKI_solvated.gro
Then in our plugin, you would use it like this:
gmx_solvate -cp 1AKI_newbox.gro -cs spc216.gro -p 1AKI_topology.top -o 1AKI_solvated.gro
This utility has extra functionality, such as if you run the command with –help then it will print out comprehensive documentation for usage. There are also two commandline flags for controlling AiiDA parameters that are not native to gromacs. These are:
- --code
This allows you to specify different gromacs installs, either local or remote or different versions
- --description
This allows you to specify a short description of the command operation for metadata, you should provide this in quotes on the commandline.
An example specifying gromacs on the local PC is below:
gmx_solvate --code gmx@localhost -cp 1AKI_newbox.gro -cs spc216.gro -p 1AKI_topology.top -o 1AKI_solvated.gro