Mercurial > repos > fmercuri > gmx_em_daimoners
comparison macros.xml @ 1:c34986976856 draft default tip
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| author | fmercuri |
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| date | Mon, 28 Jun 2021 08:59:17 +0000 |
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| 0:c581846ec2cb | 1:c34986976856 |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">2020.4</token> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> | |
| 6 </requirements> | |
| 7 </xml> | |
| 8 <xml name="citations"> | |
| 9 <citations> | |
| 10 <citation type="doi">10.1016/j.softx.2015.06.001</citation> | |
| 11 </citations> | |
| 12 </xml> | |
| 13 <xml name="md_inputs"> | |
| 14 | |
| 15 <conditional name="mdp"> | |
| 16 <param name="mdpfile" type="select" label="Parameter input"> | |
| 17 <option value="custom">Upload own MDP file</option> | |
| 18 <option value="default">Use default (partially customisable) setting</option> | |
| 19 </param> | |
| 20 <when value="custom"> | |
| 21 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/> | |
| 22 </when> | |
| 23 <when value="default"> | |
| 24 <param argument="integrator" type="select" label="Choice of integrator"> | |
| 25 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> | |
| 26 <option value="sd">Stochastic dynamics integrator</option> | |
| 27 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> | |
| 28 </param> | |
| 29 <param argument="constraints" type="select" label="Bond constraints (constraints)"> | |
| 30 <option value="none">No constraints except for those defined explicitly in the topology (none).</option> | |
| 31 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> | |
| 32 <option value="all-bonds">All bonds (all-bonds).</option> | |
| 33 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> | |
| 34 <option value="all-angles">All bonds and angles (all-angles).</option> | |
| 35 </param> | |
| 36 <param argument="cutoffscheme" type="select" label="Neighbor searching"> | |
| 37 <option value="Verlet">Generate a pair list with buffering.</option> | |
| 38 <option value="group">Generate a pair list for groups of atoms.</option> | |
| 39 </param> | |
| 40 <param argument="coulombtype" type="select" label="Electrostatics"> | |
| 41 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> | |
| 42 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> | |
| 43 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> | |
| 44 </param> | |
| 45 | |
| 46 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" /> | |
| 47 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> | |
| 48 <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." /> | |
| 49 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> | |
| 50 <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."/> | |
| 51 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> | |
| 52 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> | |
| 53 | |
| 54 </when> | |
| 55 | |
| 56 </conditional> | |
| 57 | |
| 58 </xml> | |
| 59 | |
| 60 <xml name="log"> | |
| 61 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> | |
| 62 </xml> | |
| 63 | |
| 64 <xml name="log_outputs"> | |
| 65 <data name="report" format="txt" from_work_dir="verbose.txt"> | |
| 66 <filter>capture_log</filter> | |
| 67 </data> | |
| 68 </xml> | |
| 69 | |
| 70 <xml name="test_params"> | |
| 71 <param name="mdpfile" value="default" /> | |
| 72 <param name="step_length" value="0.002"/> | |
| 73 <param name="md_steps" value="500"/> | |
| 74 <param name="write_freq" value="50"/> | |
| 75 <param name="temperature" value="300"/> | |
| 76 <param name="integrator" value="md" /> | |
| 77 <param name="constraints" value="all-bonds"/> | |
| 78 <param name="cutoffscheme" value="Verlet" /> | |
| 79 <param name="coulombtype" value="PME" /> | |
| 80 <param name="rlist" value="1.0" /> | |
| 81 <param name="rcoulomb" value="1.0" /> | |
| 82 <param name="rvdw" value="1.0" /> | |
| 83 </xml> | |
| 84 </macros> |