--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/md.xml	Thu Oct 04 18:23:17 2018 -0400
@@ -0,0 +1,154 @@
+<tool id="gmx_md" name="GROMACS production simulation" version="@VERSION@">
+    <description>for data collection</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #if $mdp.mdpfile == "custom":
+            ln -s '$mdp.mdp_input' ./md.mdp &&
+        #end if
+        #if $mdp.mdpfile == "default":
+            ln -s '$md' ./md.mdp &&
+        #end if
+
+        ln -s '$gro_input' ./npt.gro &&
+        ln -s '$cpt_input' ./npt.cpt &&
+        ln -s '$top_input' ./top_input.top &&
+        
+
+        gmx grompp -f ./md.mdp -c ./npt.gro -t ./npt.cpt -p ./top_input.top -o md_0_1.tpr &>> verbose.txt &&
+        gmx mdrun -deffnm md_0_1 &>> verbose.txt
+ 
+        #if $str == 'pdb' or $str == 'both'
+            && gmx editconf -f md_0_1.gro -o md_0_1.pdb &>> verbose.txt
+        #end if
+
+
+    ]]></command>
+        <configfiles>
+            <!-- .mdp file for the gromacs simulation -->
+            <configfile name="md">
+                #if $mdp.mdpfile == 'default':
+                    title    = OPLS Lysozyme MD simulation 
+                    ; Run parameters
+                    integrator  = $mdp.integrator    ; leap-frog integrator
+                    nsteps    = $mdp.md_steps  ; 2 * 500000 = 1000 ps (1 ns)
+                    dt        = $mdp.step_length    ; 2 fs
+                    ; Output control
+                    nstxout            = $mdp.write_freq    ; save coordinates every 10.0 ps
+                    nstvout            = $mdp.write_freq    ; save velocities every 10.0 ps
+                    nstenergy          = $mdp.write_freq    ; save energies every 10.0 ps
+                    nstlog            = $mdp.write_freq    ; update log file every 10.0 ps
+                    nstxout-compressed  = $mdp.write_freq      ; save compressed coordinates every 10.0 ps
+                                                    ; nstxout-compressed replaces nstxtcout
+                    compressed-x-grps   = System    ; group(s) to write to the compressed trajectory file
+                    ; Bond parameters
+                    continuation          = yes    ; Restarting after NPT 
+                    constraint_algorithm    = lincs      ; holonomic constraints 
+                    constraints              = $mdp.constraints  ; all bonds (even heavy atom-H bonds) constrained
+                    lincs_iter              = 1        ; accuracy of LINCS
+                    lincs_order              = 4        ; also related to accuracy
+                    ; Neighborsearching
+                    cutoff-scheme   = $mdp.cutoffscheme
+                    ns_type        = grid    ; search neighboring grid cells
+                    nstlist        = 10      ; 20 fs, largely irrelevant with Verlet scheme
+                    rcoulomb      = $mdp.rcoulomb    ; Short-range electrostatic cut-off
+                    rlist       = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
+                    rvdw        = $mdp.rvdw    ; Short-range Van der Waals cut-off
+                    ; Electrostatics
+                    coulombtype      = $mdp.coulombtype    ; method for electrostatics calculations e.g. PME
+                    pme_order      = 4        ; cubic interpolation
+                    fourierspacing  = 0.16    ; grid spacing for FFT
+                    ; Temperature coupling is on
+                    tcoupl    = V-rescale              ; modified Berendsen thermostat
+                    tc-grps    = Protein Non-Protein  ; two coupling groups - more accurate
+                    tau_t    = 0.1    0.1          ; time constant, in ps
+                    ref_t    = $mdp.temperature $mdp.temperature           ; reference temperature, one for each group, in K
+                    ; Pressure coupling is on
+                    pcoupl            = Parrinello-Rahman      ; Pressure coupling on in NPT
+                    pcoupltype          = isotropic              ; uniform scaling of box vectors
+                    tau_p            = 2.0                ; time constant, in ps
+                    ref_p            = 1.0                ; reference pressure, in bar
+                    compressibility     = 4.5e-5              ; isothermal compressibility of water, bar^-1
+                    ; Periodic boundary conditions
+                    pbc    = xyz    ; 3-D PBC
+                    ; Dispersion correction
+                    DispCorr  = EnerPres  ; account for cut-off vdW scheme
+                    ; Velocity generation
+                    gen_vel    = no    ; Velocity generation is off
+                #end if
+            </configfile>
+
+        </configfiles>
+    <inputs>
+        <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
+        <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
+        <param argument="cpt_input" type="data" format='cpt' label="Checkpoint (CPT) file from NVT run."/>
+        
+        <expand macro="md_inputs"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="gro" from_work_dir="md_0_1.gro">
+            <filter>str == 'gro' or str == 'both'</filter>
+        </data>
+        <data name="output2" format="pdb" from_work_dir="md_0_1.pdb">
+            <filter>str == 'pdb' or str == 'both'</filter>
+        </data>
+        <data name="output3" format="trr" from_work_dir="md_0_1.trr">
+            <filter>traj == 'trr' or traj == 'both'</filter>
+        </data>
+        <data name="output4" format="xtc" from_work_dir="md_0_1.xtc">
+            <filter>traj == 'xtc' or traj == 'both'</filter>
+        </data>
+
+        <data name="report" format="txt" from_work_dir="verbose.txt">
+            <filter>capture_log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gro_input" value="npt.gro" />
+            <param name="top_input" value="topol_solv.top" />
+            <param name="cpt_input" value="npt.cpt" />
+            <param name="traj" value="trr"/>
+            <param name="str" value="both"/>
+            
+            <expand macro="test_params"/>
+
+            <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
+            <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
+            <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="gro_input" value="npt.gro" />
+            <param name="top_input" value="topol_solv.top" />
+            <param name="cpt_input" value="npt.cpt" />
+            <param name="itp_input" value="posres.itp" />
+            <param name="traj" value="xtc"/>
+            <param name="str" value="pdb"/>
+            
+            <expand macro="test_params"/>
+            
+            <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
+            <output name="output4" file="md_0_1.xtc" ftype="xtc" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="gro_input" value="npt.gro" />
+            <param name="top_input" value="topol_solv.top" />
+            <param name="cpt_input" value="npt.cpt" />
+            <param name="mdpfile" value="custom" />
+            <param name="mdp_input" value="md.mdp" />
+            <param name="traj" value="trr"/>
+            <param name="str" value="gro"/>
+            <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
+            <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Upload GRO and TOP files for the production simulation, as well as the checkpoint (CPT) file from the NPT equilibration. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/online/mdp_opt.html for more information on the options.
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>