Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy1 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy0 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.4+galaxy1 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.4+galaxy0 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy1 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.5 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.3 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.2 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.1 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1 |
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2018.2 |
gmx_solvate |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
gromacs | 2022 | package |
Additional information about this tool |
ln -s '$ions' ./ions.mdp && ln -s '$gro_input' ./gro_input.gro && ln -s '$top_input' ./top_input.top && gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn '$mxw' &>> verbose.txt #if $neutralise or $conc: ## else this step would do nothing && echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc -seed $seed &>> verbose.txt && mv solv_ions.gro solv.gro #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
gro_input: newbox.gro top_input: topol.top water_model: spc216 neutralise: -neutral conc: 1 |
name: value name: value |
newbox.gro topol.top value |
Test-2 |
gro_input: newbox.gro top_input: topol.top water_model: spc216 neutralise: conc: 0 |
name: value |
newbox.gro topol.top value |