fahda-logfile

A logfile contains information about all data points of every simulation.

Download

You can download a zip file of the source from here. You can also use the git clone command to get the files.

git clone https://github.com/sorinlab/fahda-logfile
cd fahda-logfile
git submodule init
git submodule update

logfile-make.pl

An "all-frame" pdb file is generated for each simulation using trjconv. Parsing the "TITLE" lines in this file gives all the possible frames within a simulation.

# `echo 1` to select the "protein" group
echo 1 | trjconv -s frame0.tpr -f trj.xtc -o output.pdb

head output.pdb
# output.pdb
REMARK    GENERATED BY TRJCONV
TITLE     41361 t= 10500.00000
REMARK    THIS IS A SIMULATION BOX
CRYST1   75.058   75.058   75.058  90.00  90.00  90.00 P 1           1
MODEL      107
ATOM      1  H5T RG5     1      42.420  55.930  40.590  1.00  0.00
ATOM      2  O5' RG5     1      43.060  55.840  39.880  1.00  0.00
ATOM      3  C5' RG5     1      44.060  56.830  39.900  1.00  0.00
ATOM      4 H5'1 RG5     1      44.170  57.320  40.870  1.00  0.00
ATOM      5 H5'2 RG5     1      43.820  57.610  39.170  1.00  0.00

# USAGE

usegromacs33
./logfile-make.pl PROJ1797 output.log

head output.log
#output.log
1797       0       1         0
1797       0       1       100
1797       0       1       200
1797       0       1       300
1797       0       1       400
...

logfile_check.py

logfile_check.py looks for the following issues in the logfile.

1. Missing timestamps (timestamp zero included)
2. Duplicate timestamps
3. Last timestamp is not a multiple of 1000

Usage

logfile_check.py is targeted at python3.

# print help info
./logfile_check.py -h

./logfile_check.py fah.log report.txt

Development

logfile_check_test.py contains test cases that try to cover multiple scenarios for the primary methods in logfile_check.py. To run the test, you will need to install pytest via pip3.

sudo pip3 install -U pytest
pytest -v logfile_check_test.py