| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.5.1 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.3 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.2 |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.1 |
| gmx_sim |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gromacs | 2021.3 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gro_input: str_ions.gro top_input: topol_md.top inps|cpt_in: npt.cpt outps|traj: trr outps|str: gro outps|tpr_out: true sets|ensemble: npt sets|mdp|mdp_input: md.mdp sets|mdp|mdpfile: custom |
name: value name: value name: value |
str_ions.gro topol_md.top npt.cpt md.mdp value |
| Test-2 |
gro_input: str_ions.gro top_input: topol_md.top inps|cpt_in: npt.cpt outps|traj: trr outps|str: both sets|ensemble: npt sets|mdp|integrator: md sets|mdp|constraints: all-bonds sets|mdp|cutoffscheme: Verlet sets|mdp|coulombtype: PME sets|mdp|temperature: 300 sets|mdp|step_length: 0.002 sets|mdp|write_freq: 50 sets|mdp|rcoulomb: 1.0 sets|mdp|rlist: 1.0 sets|mdp|rvdw: 1.0 sets|mdp|md_steps: 500 sets|mdp|mdpfile: default |
name: value name: value name: value |
str_ions.gro topol_md.top npt.cpt value |
| Test-3 |
gro_input: str_ions.gro top_input: topol_md.top inps|cpt_in: npt.cpt inps|ndx_in: index.ndx outps|traj: trr outps|str: both sets|ensemble: npt sets|mdp|integrator: md sets|mdp|constraints: all-bonds sets|mdp|cutoffscheme: Verlet sets|mdp|coulombtype: PME sets|mdp|temperature: 300 sets|mdp|step_length: 0.002 sets|mdp|write_freq: 50 sets|mdp|rcoulomb: 1.0 sets|mdp|rlist: 1.0 sets|mdp|rvdw: 1.0 sets|mdp|md_steps: 500 sets|mdp|mdpfile: default |
name: value name: value name: value |
str_ions.gro topol_md.top npt.cpt index.ndx value |
| Test-4 |
gro_input: str_ions.gro top_input: topol_md.top inps|itp_in: posres.itp outps|traj: xtc outps|str: pdb outps|cpt_out: true sets|ensemble: nvt sets|mdp|integrator: md sets|mdp|constraints: all-bonds sets|mdp|cutoffscheme: Verlet sets|mdp|coulombtype: PME sets|mdp|temperature: 300 sets|mdp|step_length: 0.002 sets|mdp|write_freq: 50 sets|mdp|rcoulomb: 1.0 sets|mdp|rlist: 1.0 sets|mdp|rvdw: 1.0 sets|mdp|md_steps: 500 sets|mdp|mdpfile: default |
name: value name: value name: value |
str_ions.gro topol_md.top posres.itp value |