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0.README
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0.README
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# 0. Start cleaning the directory>
# chmod +x z.clean.sh ; ./z.clean.sh ; chmod -x z.clean.sh
# 1. Evaluation of aam used for simulation to detect match with the correct aam structure.
echo 1.aam_data.sh
chmod +x ./1.aam_data.sh
./1.aam_data.sh > 1.aam_data.log
# - The script will generate an output called 1.aam_data.log, where it will be shown if the structure is different ("YES") or not ("NO").
# - Create an excel file with the output 1.valid_data.txt.
# 2. Combine the rdf files in a unique directory. During the calculation just curves greater than specific number of point will be considered.
# - Notes:
# - The "minimum distance" in 2.combine_data.log should be an int number.
# - The script should assign to all rdf files the same number of row, else something is wrong! Pay attetion to it!!! All next calculation depends on that.
# - The script depends on the previous output 1.valid_data.txt.
echo 2.combine_data.sh
chmod +x ./2.combine_data.sh
./2.combine_data.sh > 2.combine_data.log
# - The output generated 2.total_number_curves.log will show the total number of curves per condition.
# - The output 2.curves_bad.dat will show curves with problems of sampling
# - Use this command for excel file
# cut -d " " -f5,8 2.total_number_curves.log | cut -d "/" -f1,9,10 | sed 's/\// /g'
# 3. Convert rdf to pmf (3.pmf.py), compare curves (3.comparison.py), and remove redudant information (3.remove_rep.sh).
echo 3.convert_rdf2pmf.sh
chmod +x 3.convert_rdf2pmf.sh
./3.convert_rdf2pmf.sh > 3.convert_rdf2pmf.log # Will call the three different scripts.
#- Used next command for excel file
# cut -f2 3.total_number_curves_no-redundant.log
# 4. Calculate the average between pmf curves.
echo 4.calculate_average.sh
chmod +x 4.calculate_average.sh
./4.calculate_average.sh > 4.calculate_average.log
# 5. Calculate curves with different bin
echo 5.calculate_bin.sh
chmod +x 5.calculate_bin.sh
./5.calculate_bin.sh > ./5.calculate_bin.log
# 6. Make figures to test how is going so far.
echo 6.figures.sh
chmod +x 6.figures.sh
./6.figures.sh
# 7. Now is time to calculate the deviation using sets of curves.
echo 7.deviation.sh
chmod +x 7.deviation.sh
./7.deviation.sh
# 8. One more test to check how is getting the plots based on the outputs of 7.deviation.sh.
chmod +x 8.figures.sh
echo 8.figures.sh
./8.figures.sh
# 9. To calculate the virial, we should separate in sets of curves the three contributions [total and vdw (estimated by 7.deviation.sh), and electrostatic (computed with the script in python 9.contributions.py)]. The next script will create all these files in the folder #oligomer#_electrostatic for each virus. Then, the virial will be estimated.
# - Notes:
# - This script just will calculate the virial and electrostatic part based on the best bin and number of curves suitable!
chmod +x 9.virial.sh
echo 9.virial.sh
./9.virial.sh
# - This script will create csv, log, and xvg files too.