Outputs and Files

StreaMD organizes each run into predictable folders with logs, intermediates, and analysis outputs.

Logs

  • log_*protein-fname*_*ligand-fname*_*cofactor-fname*_*start-time*.log: StreaMD status, warnings, and errors

  • streamd_bash_*protein-fname*_*ligand-fname*_*cofactor-fname*_*start-time*.log: stdout from GROMACS and Antechamber

Detailed logs for each ligand/cofactor preparation runs

  • md_preparation/ligands/ligandN/streamd_bash_*protein-fname*_*ligand-fname*_*cofactor-fname*_*start-time*.log: stdout for Antechamber or Gaussian ligand preparation run

  • md_preparation/cofactors/cofactorN/streamd_bash_*protein-fname*_*ligand-fname*_*cofactor-fname*_*start-time*.log: stdout for Antechamber or Gaussian cofactor preparation run

Directory Layout

Each run creates in the working directory (or current directory if --wdir is not set):

md_files/
- md_preparation/
 -- protein/
 -- ligands/
 -- cofactors/
- md_run/
 -- protein-id_ligand-id_replicaN
 --- md_analysis

md_preparation/protein/

protein.gro  posre.itp  topol.top

For multiple chains:

protein.gro
topol.top
posre_Protein_chain_A.itp
posre_Protein_chain_B.itp
topol_Protein_chain_A.itp
topol_Protein_chain_B.itp

md_preparation/ligands/

all_resid.txt

ligand_1/
ligand_1.frcmod  ligand_1.lib     ligand_1.top        sqm.in
ligand_1.gro     ligand_1.mol     leap.log            sqm.out
ligand_1.inpcrd  ligand_1.mol2    posre_ligand_1.itp  sqm.pdb
ligand_1.itp     ligand_1.prmtop  resid.txt           tleap.in
streamd_bash_1o2i_H_HIS_ligand_1_date.log

ligand_2/
...

md_preparation/cofactors/

all_resid.txt

cofactor_1/
cofactor_1.frcmod  cofactor_1.lib     cofactor_1.top        sqm.in
cofactor_1.gro     cofactor_1.mol     leap.log              sqm.out
cofactor_1.inpcrd  cofactor_1.mol2    posre_cofactor_1.itp  sqm.pdb
cofactor_1.itp     cofactor_1.prmtop  resid.txt             tleap.in
streamd_bash_1o2i_H_HIS_cofactor_1_date.log

cofactor_2/
...

md_preparation/systems/

protein_H_HIS_ligand_1.itp  complex.gro  ions.tpr   minim.mdp   nvt.mdp                     solv.gro                         topol.top
all.itp                     index.ndx    md.mdp     newbox.gro  posre_protein_ligand_1.itp  solv_ions.gro
all_ligand_resid.txt        ions.mdp     mdout.mdp  npt.mdp     posre.itp                   streamd_bash_protein_HIS_ligand_1_date.log

md_run/<system>[_replicaN]/

ligand_1.itp          em.trr       ions.tpr    md_out.edr         md_out.tpr             npt.cpt   npt.tpr  nvt.log
cofactor_1.itp        em.edr       frame.pdb   md_out.gro         md_out.xtc             npt.edr   npt.trr  nvt.mdp  topol.top
all.itp               em.gro       md_fit.xtc  md_out.log         md_short_forcheck.xtc  npt.gro   nvt.cpt  nvt.tpr  nvt.edr  solv.gro
complex.gro           em.tpr       ions.mdp    md_out.cpt         newbox.gro             npt.mdp   npt.log  index.ndx
all_ligand_resid.txt  em.log       md_fit.xtc  md_out.xtc         mdout.mdp              minim.mdp npt.tpr  posre.itp solv_ions.gro

Analysis Outputs

md_analysis/

  • potential_*.{csv,png,xtc}: potential energy from energy minimization (gmx energy)

  • temperature_*.{csv,png,xtc}: system temperature during NVT

  • density_*.{csv,png,xtc}: total density during NPT

  • pressure_*.{csv,png,xtc}: system pressure during NPT

  • rmsd_*.{csv,png}: RMSD for backbone, ligand, and active site (5 A default)

  • rmsf_*.{csv,png,xtc,pdb}: RMSF traces and structures

  • gyrate_*.{csv,png,xtc}: radius of gyration

See MM-PBSA/MM-GBSA Calculations for MM-PBSA/MM-GBSA outputs, ProLIF (Protein-Ligand Interaction Fingerprints) Analysis for interaction fingerprints, and Trajectory Convergence Analysis for RMSD convergence analysis.

MD Outputs

md_run/<system>/

  • md_fit.xtc: PBC-removed, protein- or protein-ligand-fitted trajectory

  • md_short_forcheck.xtc: short trajectory for sanity checks

  • frame.pdb: starting frame (0.1 ns)

  • last_frame.pdb: last frame of the trajectory

  • Standard GROMACS files (md_out.*, em.*, nvt.*, npt.*, index.ndx, topol.top, etc.)