The attached files are from a workflow I used with CHARMM to count water transits through a bilayer. It assumes that any drift in z has been removed by some alignment procedure that ensures the bilayer is intact and centered at a known position. Briefly,
  • watchk.inp :: identifies waters that visit the bilayer midplane region, creates a log file
  • BldWatEnt.csh :: processes the log file to get a unique list of RESIDs, and creates a stream file of ENTER commands for use with CORREL
  • wtrans.inp :: creates time series of z coord for identified waters using the stream file from BldWatEnt.csh, one file per water in a subdir (env var $ZWAT)
  • wtransits.f90 :: Fortran90 program that analyzes the water z time series produced, and reports on true transits

The idea is to greatly reduce the number of water molecules to consider explicitly by determining which ones actually visit the hydrophobic midplane region in the initial screening (watchk.inp).

The Fortran program expects command line args, and gives a brief help message when none are provided.

(The .txt extensions should be removed before use; make sure the .csh file has execute permission.)

Attached Images
watchk.inp.txt (1.03 KB, 588 downloads)
BldWatEnt.csh.txt (358 Bytes, 568 downloads)
wtrans.inp.txt (663 Bytes, 1503 downloads)
wtransits.f90.txt (7.11 KB, 761 downloads)

Rick Venable
computational chemist