Mercurial > repos > chemteam > gmx_em
comparison minim.xml @ 14:d532b7e5f64b draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
| author | chemteam |
|---|---|
| date | Wed, 29 Sep 2021 07:43:54 +0000 |
| parents | 55918daa5651 |
| children | 59c662ca4211 |
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| 13:f5d979cb4b54 | 14:d532b7e5f64b |
|---|---|
| 29 ; minim.mdp - used as input into grompp to generate em.tpr | 29 ; minim.mdp - used as input into grompp to generate em.tpr |
| 30 integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization) | 30 integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization) |
| 31 emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value | 31 emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value |
| 32 emstep = $mdp.emstep ; Energy step size | 32 emstep = $mdp.emstep ; Energy step size |
| 33 nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform | 33 nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform |
| 34 gen-seed = $mdp.seed ; random seed | |
| 34 | 35 |
| 35 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions | 36 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions |
| 36 nstlist = 1 ; Frequency to update the neighbor list and long range forces | 37 nstlist = 1 ; Frequency to update the neighbor list and long range forces |
| 37 cutoff-scheme = $mdp.cutoffscheme | 38 cutoff-scheme = $mdp.cutoffscheme |
| 38 ns_type = grid ; Method to determine neighbor list (simple, grid) | 39 ns_type = grid ; Method to determine neighbor list (simple, grid) |
| 76 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> | 77 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> |
| 77 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> | 78 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> |
| 78 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" /> | 79 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" /> |
| 79 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" /> | 80 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" /> |
| 80 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> | 81 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> |
| 82 <param argument="seed" type="integer" label="Random seed" value="1" min="-1" help="Select a random seed for initial velocity generation. Set to -1 to generate a seed." /> | |
| 81 </when> | 83 </when> |
| 82 </conditional> | 84 </conditional> |
| 83 <expand macro="log" /> | 85 <expand macro="log" /> |
| 84 </inputs> | 86 </inputs> |
| 85 <outputs> | 87 <outputs> |
| 86 <data name="output1" format="gro" from_work_dir="em.gro"/> | 88 <data name="output1" format="gro" from_work_dir="em.gro" label="GROMACS energy minimization (GRO) on ${on_string}"/> |
| 87 <data name="output2" format="edr" from_work_dir="em.edr"/> | 89 <data name="output2" format="edr" from_work_dir="em.edr" label="GROMACS energy minimization (EDR) on ${on_string}"/> |
| 88 <expand macro="log_outputs" /> | 90 <expand macro="log_outputs" /> |
| 89 </outputs> | 91 </outputs> |
| 90 <tests> | 92 <tests> |
| 91 <test> | 93 <test> |
| 92 <param name="gro_input" value="str_ions.gro" /> | 94 <param name="gro_input" value="str_ions.gro" /> |
| 93 <param name="top_input" value="topol_solv.top" /> | 95 <param name="top_input" value="topol_md.top" /> |
| 94 <param name="mdpfile" value="default" /> | 96 <param name="mdpfile" value="default" /> |
| 95 <param name="integrator" value="steep" /> | 97 <param name="integrator" value="steep" /> |
| 96 <param name="cutoffscheme" value="Verlet" /> | 98 <param name="cutoffscheme" value="Verlet" /> |
| 97 <param name="coulombtype" value="PME" /> | 99 <param name="coulombtype" value="PME" /> |
| 98 <param name="rcoulomb" value="1.0" /> | 100 <param name="rcoulomb" value="1.0" /> |
| 99 <param name="rlist" value="1.0" /> | 101 <param name="rlist" value="1.0" /> |
| 100 <param name="md_steps" value="50000" /> | 102 <param name="md_steps" value="50000" /> |
| 101 <param name="emtol" value="1000.0" /> | 103 <param name="emtol" value="1000.0" /> |
| 102 <param name="emstep" value="0.01" /> | 104 <param name="emstep" value="0.01" /> |
| 103 <output name="output1" ftype="gro" > | 105 <output name="output1" file="minim.gro" ftype="gro" lines_diff="20" /> |
| 104 <assert_contents> | |
| 105 <has_size value="4281" /> | |
| 106 </assert_contents> | |
| 107 </output> | |
| 108 <output name="output2" ftype="edr" > | 106 <output name="output2" ftype="edr" > |
| 109 <assert_contents> | 107 <assert_contents> |
| 110 <!-- this binary can vary in size a lot unfortunately --> | 108 <has_size value="5644"/> |
| 111 <has_size value="5000" delta="1000" /> | |
| 112 </assert_contents> | 109 </assert_contents> |
| 113 </output> | 110 </output> |
| 114 </test> | 111 </test> |
| 115 <test> | 112 <test> |
| 116 <param name="gro_input" value="str_ions.gro" /> | 113 <param name="gro_input" value="str_ions.gro" /> |
| 117 <param name="top_input" value="topol_solv.top" /> | 114 <param name="top_input" value="topol_md.top" /> |
| 118 <param name="mdpfile" value="custom" /> | 115 <param name="mdpfile" value="custom" /> |
| 119 <param name="mdp_input" value="minim.mdp" /> | 116 <param name="mdp_input" value="minim.mdp" /> |
| 120 <output name="output1" ftype="gro" > | 117 <output name="output1" file="minim.gro" ftype="gro" lines_diff="20" /> |
| 121 <assert_contents> | |
| 122 <has_size value="4281" /> | |
| 123 </assert_contents> | |
| 124 </output> | |
| 125 <output name="output2" ftype="edr" > | 118 <output name="output2" ftype="edr" > |
| 126 <assert_contents> | 119 <assert_contents> |
| 127 <!-- this binary can vary in size a lot unfortunately --> | 120 <has_size value="5644"/> |
| 128 <has_size value="5000" delta="1000" /> | |
| 129 </assert_contents> | 121 </assert_contents> |
| 130 </output> | 122 </output> |
| 131 </test> | 123 </test> |
| 132 | 124 |
| 133 </tests> | 125 </tests> |