Workflow

Molecular model

dps pdb2dps creates an initial coarse-grained conformation and ITP topology from a protein sequence. The topology can then be refined with dps genelastic, dps addangle, or dps modifyres. Use dps pdb2bond when a PDB file needs CONECT records derived from the DROPPS topology.

System model

dps genmesh packs one or more molecule types onto a three-dimensional mesh and emits a system coordinate file and TOP topology. dps editconf changes the orthorhombic box and can unwrap coordinates along selected axes.

Run preparation

dps grompp combines PDB coordinates, TOP/ITP topology, and MDP parameters into a TPR v2 run input:

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

This is the point at which force-field compatibility, topology completeness, bead ordering, masses and charges, periodic-box geometry, and the minimum-image cutoff requirement are validated. Fix reported input errors instead of bypassing them.

Simulation and restart

Start a run with:

dps mdrun -s run.tpr -o run

Operational settings such as platform, device, precision, wall-clock limit, and checkpoint cadence can be selected at launch; scientific settings remain in the TPR. By default, restart files are refreshed every five wall-clock minutes and once more at clean termination:

  • run.chk: an exact, platform-dependent OpenMM checkpoint;

  • run.state.xml: a portable OpenMM State; and

  • run.restart.json: checksums and compatibility metadata.

Resume using the prefix’s default checkpoint:

dps mdrun -s run.tpr -o run -cpi

Keep all three restart files together. A native checkpoint provides the most exact continuation when OpenMM version, platform, hardware, and system match. DROPPS can use the paired State XML when native-checkpoint compatibility has changed. The MDP nsteps value remains the target total production step, not an additional number of steps.

Trajectory preparation

dps trjconv handles trajectory selection, time subsetting, periodic-boundary reconstruction, centering, fitting, and XTC/PDB conversion. For example:

dps trjconv -s run.tpr -f run.xtc -o frame.pdb \
  -b 100 -e 100 -sel "group 0"

Create reusable atom groups with dps make_ndx and inspect files before analysis with dps check. The dps gsd2xtc command imports GSD trajectories when required.

Analysis

DROPPS provides density profiles, contact maps, inter- and intramolecular distances, radii of gyration, backbone angles, mean-square displacement, RMSD, assembly statistics, phase exchange, contact statistics, energy extraction, and rerun energy evaluation. Start with Command reference; each page contains the exact 1.0 command options.