Galaxy |

GROMACS initial setup tool metadata

Miscellaneous

Name: GROMACS initial setup

Description: of topology and GRO structure file

Id: gmx_setup

Guid: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2022+galaxy0

Version: 2022+galaxy0

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2022+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2021.3+galaxy0

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.4+galaxy0

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.2+galaxy0

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.5

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.3

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.2

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.1

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1

toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2018.2

gmx_setup

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

gromacs

2022

package

Additional information about this tool

Command:

ln -s '$pdb_input' ./pdb_input.pdb &&
        gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water $water -ff $ff -${ignore_h}ignh -merge all &>> verbose.txt

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

pdb_input: init.pdb
water: spce
ff: oplsaa
ignore_h: False

name: value
name: value
name: value

init.pdb
value