Input Files

DROPPS uses a structured set of input files that work together to define a complete coarse-grained simulation system. This page explains the four most important file types used in DROPPS:

  1. PDB files (coordinates)

  2. MDP files (MD parameters)

  3. ITP files (single-chain topology)

  4. TOP files (system-level topology)

These files are ultimately combined using dps grompp to produce a DROPPS .tpr file.

Each section below describes the purpose, format, and role of each file.

PDB File (Structure)

PDB files store coordinates and chain information for coarse-grained simulations. They are used at multiple points in the workflow:

  • Generated by dps pdb2dps for single-chain CG structures.

  • Used by dps genmesh to assemble multichain systems.

  • Passed to dps grompp as the final coordinate input.

A typical DROPPS CG PDB structure contains:

  • Atom names representing coarse-grained beads

  • Residue names matching HPS (or other CG) residue labels

  • Chain IDs for multi-chain systems

  • ONE bead per residue (for HPS-type FFs)

Example (CG PDB snippet):

ATOM      1   ALA A   1      12.541  15.223  10.991
ATOM      2   PRO A   2      13.114  16.102  11.887
ATOM      3   LYS A   3      14.001  16.445  12.901

Important notes:

  • Coordinates may be scaled or centered using dps editconf.

  • Multi-chain PDBs generated by genmesh contain possibly hundreds of chains arranged on a regular lattice.

MDP File (Simulation Parameters)

MDP files define the simulation control parameters, analogous to GROMACS .mdp files, but interpreted by DROPPS to generate an OpenMM integrator configuration .

An MDP file contains:

  • simulation time settings

  • integrator type

  • timestep

  • thermostat parameters

  • cutoffs and neighbor lists

  • trajectories and energy output frequency

Example MDP snippet:

integrator      = langevin
dt              = 0.01
nsteps          = 5000000
tau_t           = 1.0
temperature     = 310
cutoff-scheme   = hps
output-frequency = 10000

Notes:

  • DROPPS parses the MDP using its internal mdp_reader module.

  • Not all GROMACS keywords are supported; DROPPS supports LLPS-relevant parameters specifically.

  • The MDP file is combined with PDB + ITP + TOP during grompp to form the .tpr.

Please refer to Reference Manual for detailed mdp setups.

ITP File (Single-Chain Topology)

ITP files define the topology of a single coarse-grained chain. These files are created by dps pdb2dps and contain:

  • atom (bead) types

  • masses

  • charges

  • sigma / epsilon

  • bonded terms (bonds, angles, optionally dihedrals)

  • residue labels

  • mapping from residue → bead name → FF parameters

A typical DROPPS ITP file may contain:

[ atoms ]
; id  type   resnr  resid  charge  mass
  1   ALA      1     ALA     0.0    100
  2   PRO      2     PRO     0.0    100
  3   LYS      3     LYS     1.0    110

[ bonds ]
1  2  1
2  3  1

[ angles ]
1  2  3  1

Key characteristics:

  • Residue parameters come directly from the CG force field, such as HPS, M`HPS`, or your custom FF.

  • Angle terms may be optional depending on FF definition.

  • Users can modify FF parameters programmatically using pydps (page 17).

TOP File (System Topology)

The TOP file describes the entire multichain system, including:

  • which ITP files are included

  • number of chains

  • system-wide definitions

  • nonbonded parameter includes

  • global simulation topology hierarchy

A typical TOP file looks like:

#include "asyn.itp"

[ system ]
Alpha-synuclein LLPS system

[ molecules ]
asyn   125

This file is generated automatically by dps genmesh and updated during dps grompp.

Important notes:

  • The TOP file acts as the master topology.

  • DROPPS topologies resemble GROMACS .top files but contain CG-specific force-field and system metadata.

  • The final system topology is validated by dps check.

How These Files Work Together

The four primary input files flow through the simulation pipeline as follows:

  1. pdb2dps → produces *.pdb + *.itp (single-chain)

  2. genmesh → builds multi-chain *.pdb → generates system.top

  3. grompp → combines:

    • system.pdb

    • system.top

    • md.mdp

    • all included .itp files

    → produces run.tpr

  4. mdrun → runs simulation and generates:

    • run.xtc

    • run.log

    • run.ndx (optional)

This mirrors the GROMACS workflow but is specialized for LLPS simulations using CG force fields.

Summary

DROPPS input files form a coherent ecosystem:

  • PDB — coordinates for single-chain and multi-chain systems

  • MDP — simulation parameters

  • ITP — single-chain topology describing beads and bonded terms

  • TOP — system-level topology linking all chains and FF files

These files are merged by dps grompp into a DROPPS-native .tpr file, which serves as the input for dps mdrun.