Workflows

Workflow Example MDWeb is powered by a set of BioMoby Molecular Dynamics Web-Services (MDMoby).

One of the main advantages of web services is the possibility to interconnect them building complex pipelines called workflows.

To facilitate most usual MD operations, MDWeb offers a collection of pre-packed workflows. Settings have been adapted to run successfully on most systems, and their use for non-experts is recommended. However, MDWeb provides also the same functionality as separate operations, so the individual parameters could be adjusted. The pre-packed operations include:

  • Workflows for generate topologies.

  • Workflows for solvate and neutralize structures.

  • Workflows for running a complete MD Setup.

  • Workflows for equilibrate systems.

This help section shows a short description of the workflows available. Clicking on the workflow name, a new window will automatically open, showing the workflow as a graphical diagram, where input object/s, output object/s, web services and scripting pieces can be easily identified, together with the necessary interconnections.

Setup for Amber Simulation

Generate Topology for Amber

Generate Topology for Amber.
  • ForceField: Amber Parm99SB* for Proteins, Amber Parm99bsc0 for Nucleic Acids (DNA/RNA).
  • Program: Leap from AmberTools Package.
  1. Remove crystallographic water molecules.
  2. Add hydrogen atoms and missing side chain atoms as appropiate.

Amber MD Setup

Amber MD Setup. Structure Setup for AMBER Forcefield.
  • ForceField: Amber Parm99SB* for Proteins, Amber Parm99bsc0 for Nucleic Acids (DNA/RNA).
  • Programs: namd2 from NAMD Package, leap from AmberTools package, protpKa and CMIP.
  1. Generate Topology for AMBER.
  2. Protonate Histidine residues according to protpKa program algorithm.
  3. Add 20 water molecules at the energetically best favourable positions of the structure surface using CMIP program.
  4. Energy minimize hydrogen atoms for 500 steps of conjugate gradients, while the rest of the structure is kept fixed.
  5. Energy minimize the structure for 500 steps of conjugate gradients, restraining heavy atoms with a force constant of 50 Kcal/mol to their initial positions.

Amber MD Setup with Solvation

AMBER MD Setup with Solvation. Structure Setup + Solvation for AMBER Forcefield.
  • ForceField: Amber Parm99SB* for Proteins, Amber Parm99bsc0 for Nucleic Acids (DNA/RNA).
  • Programs: namd2 from NAMD Package, leap from AmberTools package, protpKa and CMIP.
  1. AMBER MD Setup.
  2. Set a truncated Octahedron box of TIP3P water molecules with a spacing distance of 15 Å around the system.
  3. Add Cl- and/or Na+ ions necessary to neutralize the system. Then, add the appropiate amount of ions up to a concentration of 50 mM.
  4. Further energy minimize the structure for 500 steps of conjugate gradients, restraining heavy atoms with a force constant of 50Kcal/mol to their initial positions.

Amber Advanced Equilibration

AMBER Advanced Equilibration. System Equilibration.
  • Equilibration steps done in NPT ensemble with Periodic Boundary Conditions.
  • Particle Mesh Ewald (PME) for full-system periodic electrostatics.
  • Constant temperature dynamics via Langevin Dynamics.
  • Constant pressure dynamics via Nose-Hoover Langevin piston.
  • SHAKE is used to maintain all bonds involving hydrogen atoms at their equilibrium values.
  1. Heat solvent to 300K. Solute atoms restrained (force constant of 10 Kcal/mol). Length 5ps.
  2. Reduce force constant to 5 Kcal/mol. Length 1ps.
  3. Reduce force constant to 2.5 Kcal/mol and limit restraints to backbone atoms. Length 1ps.
  4. Reduce force constant to 1 Kcal/mol. Length 1ps.
  5. Simulation without restraints. Length 1ps.

Amber FULL MD Setup

Complete Setup for AMBER forcefield (Structure Setup + Solvation + Equilibration).
  • ForceField: Amber Parm99SB* for Proteins, Amber Parm99bsc0 for Nucleic Acids (DNA/RNA).
  • Programs: namd2 from NAMD Package, leap from AmberTools package, protpKa and CMIP.
  • Equilibration steps done in NPT ensemble with Periodic Boundary Conditions.
  • Particle Mesh Ewald (PME) for full-system periodic electrostatics.
  • Constant temperature dynamics via Langevin Dynamics.
  • Constant pressure dynamics via Nose-Hoover Langevin piston.
  • SHAKE is used to maintain all bonds involving hydrogen atoms at their equilibrium values.
  1. AMBER MD Setup with Solvation.
  2. AMBER Advanced Equilibration.

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Setup for Gromacs Simulation

Generate Topology for Gromacs

Generate Topology for GROMACS. Generate top and itp Topology Files for Gromacs.
  • Programs: pdb2gmx from Gromacs Package.
  1. Remove crystallographic water molecules.
  2. Add side chain missing atoms using Leap from AmberTools package.
  3. Add Hydrogen atoms using pdb2gmx.

Gromacs MD Setup

GROMACS MD Setup. Structure Setup for Gromacs.
  • Programs: pdb2gmx, grompp, editconf, trjconv, make_ndx and mdrun from Gromacs Package, leap from AmberTools package, protpKa and CMIP.
  1. Generate Topology for GROMACS.
  2. Protonate Histidine residues according to protpKa program algorithm.
  3. Add 20 water molecules at the energetically best favourable positions of the structure surface using CMIP program.
  4. Energy minimize hydrogen atoms for 500 steps of hydrogen conjugate gradients, while the rest of the structure is kept fixed.
  5. Energy minimize the structure for 500 steps of structure conjugate gradients, restraining heavy atoms with a force constant of 500KJ/mol*nm2 to their initial positions.

Gromacs MD Setup with Solvation

GROMACS MD Setup with Solvation. Structure Setup + Solvation for Gromacs.
  • Programs: pdb2gmx, grompp, editconf, trjconv, make_ndx, genbox, genion and mdrun from Gromacs Package, leap from AmberTools package, protpKa and CMIP.
  1. GROMACS MD Setup.
  2. Set a truncated Octahedron box of TIP3P water molecules (Amber FF) or SPC water molecules (other FF's) with a spacing distance of 15Å around the molecule.
  3. Add Cl- and/or Na+ ions necessary to neutralize the system. Then, add the appropiate amount of ions up to a concentration of 50 mM.
  4. Further energy minimize the structure for 500 steps of conjugate gradients, restraining heavy atoms with a force constant of 500KJ/mol*nm2 to their initial positions.

Gromacs Advanced Equilibration

GROMACS Advanced Equilibration. System Equilibration.
  • Equilibration steps done in NPT ensemble with Periodic Boundary Conditions.
  • Particle Mesh Ewald (PME) for full-system periodic electrostatics.
  • Constant temperature dynamics via Velocity-rescale algorithm.
  • Constant pressure dynamics via Parrinello-Rahman algorithm.
  • LINCS Linear Constraint Solver is used to maintain all bonds at their equilibrium values.
  1. Heat solvent to 300K. Solute atoms restrained (Force constant of 400 KJ/mol*nm2. Length 5ps.
  2. Reduce force constant to 300 KJ/mol*nm2. Length 1ps.
  3. Reduce force constant to 200 KJ/mol*nm2 and limit restraints to backbone atoms. Length 1ps.
  4. Reduce force constant to 100 KJ/mol*nm2. Length 1ps.
  5. Simulation without restraints. Length 1ps.

Gromacs FULL MD Setup

GROMACS FULL MD Setup. Complete Setup for Gromacs Package (Structure Setup + Solvation + Equilibration).
  • Programs: pdb2gmx, grompp, editconf, trjconv, make_ndx, genbox, genion and mdrun from Gromacs Package, leap from AmberTools package, protpKa and CMIP.
  • Equilibration steps done in NPT ensemble with Periodic Boundary Conditions.
  • Particle Mesh Ewald (PME) for full-system periodic electrostatics.
  • Constant temperature dynamics via Velocity-rescale algorithm.
  • Constant pressure dynamics via Parrinello-Rahman algorithm.
  • LINCS Linear Constraint Solver was used to maintain all bonds at their equilibrium values.
  1. GROMACS MD Setup with Solvation.
  2. GROMACS Advanced Equilibration.

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Setup for NAMD Simulation

Generate Topology for NAMD

Generate Topology for NAMD. Generate PSF Topology for Charmm Forcefield.
  • ForceField: Charmm-27.
  • Program: psfgen from NAMD Package.
  • Warning: Ligands not allowed.
  1. Remove crystallographic water molecules.
  2. Add hydrogen atoms and missing side chain atoms as appropiate.

NAMD MD Setup

NAMD MD Setup. Structure Setup for Charmm Forcefield.
  • ForceField: Charmm-27.
  • Programs: psfgen, vmd (solvate and autoionize plugins) and namd2 from NAMD Package, protpKa and CMIP.
  1. Generate Topology for NAMD.
  2. Protonate Histidine residues according to protpKa program algorithm.
  3. Add 20 water molecules at the energetically best favourable positions of the structure surface using CMIP program.
  4. Energy minimize hydrogen atoms for 500 steps of conjugate gradients, while the rest of the structure is kept fixed.
  5. Energy minimize the structure for 500 steps of conjugate gradients, restraining heavy atoms with a force constant of 50Kcal/mol to their initial positions.

NAMD MD Setup with Solvation

NAMD MD Setup with Solvation. Structure Setup + Solvation for Charmm Forcefield.
  • ForceField: Charmm-27.
  • Programs: psfgen, vmd (solvate and autoionize plugins) and namd2 from NAMD Package, protpKa and CMIP.
  1. NAMD MD Setup.
  2. Set a cubic box of TIP3P water molecules with a spacing distance of 15 Å.
  3. Add Cl- and/or Na+ ions necessary to neutralize the system. Then, add the appropiate amount of ions up to a concentration of 50 mM.
  4. Further energy minimize the structure for 500 steps of conjugate gradients, restraining heavy atoms with a force constant of 50Kcal/mol to their initial positions.

NAMD Advanced Equilibration

NAMD Advanced Equilibration. System Equilibration.
  • Equilibration steps done in NPT ensemble with Periodic Boundary Conditions.
  • Particle Mesh Ewald (PME) for full-system periodic electrostatics.
  • Constant temperature dynamics via Langevin Dynamics.
  • Constant pressure dynamics via Nose-Hoover Langevin piston.
  • SHAKE is used to maintain all bonds involving hydrogen atoms at their equilibrium values.
  1. Heat solvent to 300K. Solute atoms restrained (force constant of 10 Kcal/mol). Length 5ps.
  2. Reduce force constant to 5 Kcal/mol. Length 1ps.
  3. Reduce force constant to 2.5 Kcal/mol and limit restraints to backbone atoms. Length 1ps.
  4. Reduce force constant to 1 Kcal/mol. Length 1ps.
  5. Simulation without restraints. Length 1ps.

NAMD FULL MD Setup

NAMD FULL MD Setup. Complete Setup for Charmm Forcefield (Structure Setup + Solvation + Equilibration).
  • ForceField: Charmm-27.
  • Programs: psfgen, vmd (solvate and autoionize plugins) and namd2 from NAMD Package, protpKa and CMIP.
  • Equilibration steps done in NPT ensemble with Periodic Boundary Conditions.
  • Particle Mesh Ewald (PME) for full-system periodic electrostatics.
  • Constant temperature dynamics via Langevin Dynamics.
  • Constant pressure dynamics via Nose-Hoover Langevin piston.
  • SHAKE is used to maintain all bonds involving hydrogen atoms at their equilibrium values.
  1. NAMD MD Setup with Solvation.
  2. NAMD Advanced Equilibration.