First Simulation

This tutorial provides a complete, step-by-step guide to performing your first molecular dynamics simulation using DROPPS.

DROPPS is intentionally designed to mimic the user interface of GROMACS, meaning that each step corresponds to a familiar GROMACS command:

GROMACS

DROPPS

gmx pdb2gmx

dps pdb2dps

gmx editconf

dps editconf

gmx grompp

dps grompp

gmx mdrun

dps mdrun

gmx make_ndx

dps make_ndx

gmx contact

dps contact

This tutorial walks you through the complete pipeline.

Overview of the Workflow

A DROPPS simulation consists of the following steps:

  1. Generate single-chain structure & topology (pdb2dps)

  2. Build a multi-chain system (genmesh)

  3. Prepare simulation input (grompp)

  4. Run MD simulation (mdrun)

  5. (Optional) Build index groups (make_ndx)

  6. (Optional) Perform trajectory analysis (contact, density, gyrate, etc.)

Each step directly corresponds to a command in the dps command-line suite.

1. Generate Structure and Topology (pdb2dps)

To create the initial single-chain structure and topology from a sequence or PDB file, use dps pdb2dps:

dps pdb2dps -f asyn.pdb -op asyn -on asyn -oc asyn

This command performs:

  • sequence parsing

  • generation of HPS bead representation

  • force-field assignment

  • writing the following files:

    • asyn.pdb — coarse-grained coordinates

    • asyn.itp — single-chain topology

    • asyn-angle.itp (optional, if angles are included)

2. Build a Multi-Chain System (genmesh)

To construct a system with many copies of the protein, use dps genmesh:

dps genmesh -f asyn.pdb -mesh 5 5 5 -n 125 -p asyn.top -o system.pdb

This command:

  • arranges 125 chains on a 5×5×5 spatial mesh

  • generates a multi-chain coordinate file (system.pdb)

  • generates or updates a system topology file (system.top)

insert-molecules in GROMACS is replaced by dps genmesh

3. Prepare MD Input (grompp)

Once the structure and topology are ready, create the simulation input file (.tpr) using:

dps grompp -m md.mdp -f system.pdb -p system.top -o asyn.tpr

This step:

  • reads md.mdp (simulation parameters)

  • reads system.pdb (coordinates)

  • reads system.top (topology)

  • generates asyn.tpr containing all integrated information

4. Run the Simulation (mdrun)

To run the MD simulation:

dps mdrun -s asyn.tpr -o asyn

The simulation will output:

  • asyn.xtc — coarse-grained trajectory

  • asyn.edr — energy file

  • asyn.log — simulation log

  • periodic screen output with step/energy summaries

This mirrors gmx mdrun but optimized for HPS simulations.

5. Generate Index Groups (Optional)

Some analyses require custom index groups.

Use:

dps make_ndx -f asyn.tpr -o asyn.ndx

The interactive interface supports:

  • splitch — automatically split groups by chain (specialized for large multichain HPS systems)

  • res, abbr, chain, index, etc.

6. Perform Data Analysis (Optional)

DROPPS provides a suite of built-in analysis tools (page 36):

  • dps density

  • dps cmap

  • dps idist / dps odist

  • dps gyrate

  • dps contact

Example: calculate a contact number map between protein chains:

dps contact -s asyn.tpr -f asyn.xtc -n asyn.ndx -o contact.xvg

Example: compute density profile along the z-axis:

dps density -s asyn.tpr -f asyn.xtc -n asyn.ndx --axis z -o rho.xvg

Complete Example Workflow

Putting everything together:

# 1. Single chain
dps pdb2dps -f asyn.pdb -op asyn -on asyn -oc asyn

# 2. Multi-chain system
dps genmesh -f asyn.pdb -mesh 5 5 5 -n 125 -p asyn.top -o system.pdb

# 3. Generate tpr
dps grompp -m md.mdp -f system.pdb -p system.top -o asyn.tpr

# 4. Run MD
dps mdrun -s asyn.tpr -o asyn

# 5. Analysis
dps contact -s asyn.tpr -f asyn.xtc -n asyn.ndx -o contact.xvg

Troubleshooting

Common issues (summarized from user guidance on pp. 31–33):

  • Command not found Ensure dps is added to your $PATH.

  • Missing topology files Check that .itp and .top files are correctly generated in earlier steps.

  • MDAnalysis cannot load trajectory Use dps check to diagnose tpr / xtc issues.

  • Incorrect box size after genmesh Use dps editconf to adjust simulation boundaries.

Summary

You have now completed your first full DROPPS simulation, following the exact pipeline recommended by the official documentation slides. The design philosophy, commands, and workflow mirror GROMACS but are optimized for multi-chain HPS coarse-grained simulations.

Next steps:

  • Learn advanced mdp parameters

  • Enable elastic restraints (dps genelastic)

  • Add angle potentials (dps addangle)

  • Write custom analysis scripts using the trajectory API