Repository revision
24:c4fbab8e03c5

Repository 'gmx_solvate'
hg clone https://toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate

GROMACS solvation and adding ions tool metadata
Miscellaneous
to structure and topology files
gmx_solvate
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0
2022+galaxy0
None
True
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

    
None
False
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