Details

anacolt

This script (analyze NAMD colvar trajectory) is intended to pars NAMD colvar trajectory files and plot/extract data from any column you like.

anamo

This script (analyze NAMD output) is intended to pars NAMD output files and plot energy, temperature, and whatever information NAMD writes down.
If you have different Values for "outputEnergies" and "outputPressure" use Time/TS if you want to plot information affected by this value. Use PTime/PTS if you want to plot Information which is affected by this keyword. I didn't test this so far. If you use it double check the resulting plot. Same applies for aMD. use aTS for the timesteps.

cattraj

This script (cat trajectory) is intended to be used on NAMD 2.8 colvars trajectory files. It's usage is similar to catdcd and the default behavior is to concatenate colvar trajectory files from consecutive runs. As with catdcd it is able to skip frames and thus reduce the time resolution. The first file read will always contain one more frame then the following files because it either includes frame zero or the last step from the previous file.

pdb2charmm

This script (PDB to CHARMM) is intended to convert/clean PDB files to CHARMM readable PDB files.
This tool gets extended as I need som more functionality.

Currently it is intended to:

  • fix missing HETATM record for specific residue names (see CONFIG section)
  • fix Engineered residues (see CONFIG section)
  • removes all residues not defined in the CONFIG section
  • renumber ATOM and RESIDUE IDs
  • Create PDB and PATCH for CHARMM from a PDB generated via H++ (http://biophysics.cs.vt.edu/H++/) to get proper protonation state

USE WITH CARE since all parts were written for a special purpose and might fail on others.
PDB file format specifications: http://www.wwpdb.org/documentation/file-format 

run_ibverbs

This script is intended to generate NAMD input files and submit consecutive jobs to SGE. It uses CHARM++ instead of MPI to run NAMD parallel jobs.
It reads the status files generated by NAMD to adjust the start timestep for the new NAMD config file to make sure the new run will start correct - even if a simulation crashed. Since I stumbled over some broken DCD files but according to the NAMD log, NAMD terminated successfully with full step count and the extended restart file also containt the right nuber of steps I added a file size check which compares the previous run with the current run.

Download files

Easy Folder Listing (molmod)

Filename Size Date & Time
A code file anacolt.py 8.44 KB 2018-06-04 21:52:40
A code file anamo.py 20.3 KB 2018-06-04 21:52:40
A code file cattraj.py 5.72 KB 2018-06-04 21:52:40
A code file pdb2charmm.py 16.2 KB 2018-06-04 21:52:40
A code file run_ibverbs.py 24.51 KB 2018-06-04 21:52:40