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1 <tool id="gmx_em" name="GROMACS energy minimization daimoners' version" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>of the system prior to equilibration and production MD</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11
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12 #if $mdp.mdpfile == 'custom':
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13 ln -s '$mdp.mdp_input' ./minim.mdp &&
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14 #else:
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15 ln -s '$minim' ./minim.mdp &&
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16 #end if
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17
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18 ln -s '$gro_input' ./solv_ions.gro &&
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19 ln -s '$top_input' ./top_input.top &&
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20
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21 gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr -maxwarn 5 &>> verbose.txt &&
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22 gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt
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23
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24 ]]></command>
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25 <configfiles>
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26 <!-- .mdp files for the gromacs simulation -->
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27 <configfile name="minim">
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28 #if $mdp.mdpfile == 'default':
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29 ; minim.mdp - used as input into grompp to generate em.tpr
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30 integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization)
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31 emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value
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32 emstep = $mdp.emstep ; Energy step size
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33 nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform
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34
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35 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
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36 nstlist = 1 ; Frequency to update the neighbor list and long range forces
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37 cutoff-scheme = $mdp.cutoffscheme
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38 ns_type = grid ; Method to determine neighbor list (simple, grid)
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39 coulombtype = $mdp.coulombtype ; Treatment of long range electrostatic interactions
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40 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
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41 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
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42 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
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43 pbc = xyz ; Periodic Boundary Conditions (yes/no)
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44 #end if
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45 </configfile>
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46 </configfiles>
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47
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48 <inputs>
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49 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
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50 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
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51 <conditional name="mdp">
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52 <param name="mdpfile" type="select" label="Parameter input">
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53 <option value="custom">Upload own MDP file</option>
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54 <option value="default">Use default (partially customisable) setting</option>
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55 </param>
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56 <when value="custom">
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57 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/>
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58 </when>
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59
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60 <when value="default">
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61 <param argument="integrator" type="select" label="Choice of integrator.">
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62 <option value="steep">Steepest descent algorithm.</option>
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63 <option value="cg">Conjugate gradient algorithm.</option>
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64 <option value="l-bfgs">Quasi-Newtonian algorithm.</option>
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65 </param>
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66 <param argument="cutoffscheme" type="select" label="Neighbor searching.">
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67 <option value="Verlet">Generate a pair list with buffering.</option>
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68 <option value="group">Generate a pair list for groups of atoms.</option>
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69 </param>
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70 <param argument="coulombtype" type="select" label="Electrostatics.">
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71 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
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72 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
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73 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
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74 </param>
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75 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
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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."/>
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77 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
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78 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" />
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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" />
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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." />
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81 </when>
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82 </conditional>
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83 <expand macro="log" />
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84 </inputs>
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85 <outputs>
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86 <data name="output1" format="gro" from_work_dir="em.gro"/>
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87 <data name="output2" format="edr" from_work_dir="em.edr"/>
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88 <expand macro="log_outputs" />
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="gro_input" value="str_ions.gro" />
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93 <param name="top_input" value="topol_solv.top" />
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94 <param name="mdpfile" value="default" />
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95 <param name="integrator" value="steep" />
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96 <param name="cutoffscheme" value="Verlet" />
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97 <param name="coulombtype" value="PME" />
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98 <param name="rcoulomb" value="1.0" />
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99 <param name="rlist" value="1.0" />
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100 <param name="md_steps" value="50000" />
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101 <param name="emtol" value="1000.0" />
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102 <param name="emstep" value="0.01" />
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103 <output name="output1" ftype="gro" >
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104 <assert_contents>
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105 <has_size value="4281" />
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106 </assert_contents>
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107 </output>
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108 <output name="output2" ftype="edr" >
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109 <assert_contents>
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110 <!-- this binary can vary in size a lot unfortunately -->
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111 <has_size value="5000" delta="1000" />
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112 </assert_contents>
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113 </output>
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114 </test>
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115 <test>
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116 <param name="gro_input" value="str_ions.gro" />
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117 <param name="top_input" value="topol_solv.top" />
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118 <param name="mdpfile" value="custom" />
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119 <param name="mdp_input" value="minim.mdp" />
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120 <output name="output1" ftype="gro" >
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121 <assert_contents>
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122 <has_size value="4281" />
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123 </assert_contents>
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124 </output>
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125 <output name="output2" ftype="edr" >
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126 <assert_contents>
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127 <!-- this binary can vary in size a lot unfortunately -->
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128 <has_size value="5000" delta="1000" />
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129 </assert_contents>
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130 </output>
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131 </test>
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132
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133 </tests>
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134 <help><![CDATA[
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135
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136 .. class:: infomark
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137
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138 **What it does**
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139
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140 This tool performs energy minimization of a system prior to a GROMACS simulation.
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141
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142 _____
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143
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144 .. class:: infomark
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145
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146 **Input**
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147
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148 - GRO structure file.
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149 - Topology (TOP) file.
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150 - MDP parameter file (optional)
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151
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152 To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options.
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153
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154 .. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
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155
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156 _____
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157
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158
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159 .. class:: infomark
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160
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161 **Output**
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162
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163 - GRO structure file.
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164
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165 ]]></help>
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166
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167 <expand macro="citations" />
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168 </tool>
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