Changelog

0.5.1 (Future release)

  • add argument salt_concentration - salt concentration in mol/L passed to gmx genion -conc (default: not set, only charge neutralization is performed)

  • add argument ion_pname - positive ion name passed to gmx genion -pname (default NA)

  • add argument ion_nname - negative ion name passed to gmx genion -nname (default CL)

  • add argument water_model - water model passed to gmx pdb2gmx -water (default tip3p)

0.5

  • add argument box_type - simulation box type (triclinic, cubic, dodecahedron, octahedron) (default cubic) defined using gmx editconf -bt

  • add argument box_padding_nm - minimum solute-to-box edge distance (default 1 nm = 10 A) defined using gmx editconf -d

0.4.1

  • added documentation

  • fixed bug with –no_dr and gaussian run

0.4

  • allow to keep all gmx_MMPBSA temporary files for debugging or for gmx_MMPBSA_ana usage (--debug argument)

  • allow to provide arguments through config.yml for run_md, run_prolif, run_gbsa

  • fix minor bug with steps - allow to run run_md steps 2,3,4 without –wdir_to_continue if step 1 is also provided

  • added gmx_MMPBSA residue decomposition analysis feature

  • add support for running replicate simulations of the same complexes

  • save the last frame into last_frame.pdb

0.3

  • Set default temperature to 300K

  • Add Position Restraints for MCPB.py pipline

  • Logo

  • Prolif draw_map point_size argument

  • Prolif and GBSA added directory column

  • Change nvt/npt/md time and seed in user-defined mdp files only if the --seed, --nvt_time, --npt_time and --md_time arguments were explicitly set up in the StreaMD arguments list otherwise user mdp parameters will be used

0.2.9

  • Prolif n_jobs automatic calculation

  • Fixed bug with interrupted continuation runs

  • Fixed bug with protein only in water simulations analysis

  • Add directory information into rmsd output files for replicate runs

  • Separate analysis output subdirectory

  • Tests added

0.2.8

  • Added n_jobs and protein_selection arguments to run_prolif

  • Added save_traj_without_water argument to run_md

0.2.7

  • Fixed an issue with ligand restraints during NPT and NVT

  • RMSD of ligand, backbone, Active Site groups are calculated by MDanalysis and saved in 1 common output file

  • Use xtc and tpr files containing no water for RMSD analysis (to prevent memory issues)

  • Added additional trajectory convergence analysis (html interactive files requires plotly)

  • Added plotly dependency in env.yml

  • Transform xvg analysis files to csv

  • Save successfully finished names of the systems to the text output file

  • Calculate MMPBSA intermediate files in tmp directories for multiple run in one directory

  • Add unique suffix for run_md and run_gbsa output files for simultaneous runs in the same working directory

0.2.6

  • Added GPU support

  • Use only available CPUs

  • Fixed logging

  • Added mdrun_per_node argument