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Electron_Density_From_Simulation.dat
Form_Factor_From_Simulation.dat
Headgroup_Glycerol_Order_Parameters_Simulation.dat
OrdPars.dat
README.md
analysis_NMRL3.py
area.dat
box.xvg
electronsCHOL.dat
electronsLIPID.dat
fitness.txt
mappingFILE.txt
mappingFILEchol.txt
sn-1_Order_Parameters_Simulation.dat
sn-2_Order_Parameters_Simulation.dat

README.md

#!/bin/bash
#Model from https://doi.org/10.5281/zenodo.166034

wget https://zenodo.org/record/166034/files/popc00_T298_every100ps.tpr
wget https://zenodo.org/record/166034/files/popc00_T298_every100ps.xtc

mv popc00_T298_every100ps.tpr topol.tpr
mv popc00_T298_every100ps.xtc traj.xtc

cp ../../../../../../MATCH/MAPPING/mappingPOPCslipids.txt ./mappingFILE.txt
awk -f ../../../../../scripts/makeELECTRONSpopc.awk mappingFILE.txt > electronsLIPID.dat

cp ../../../../../../MATCH/MAPPING/mappingCHOLESTEROLslipid.txt ./mappingFILEchol.txt
awk -f ../../../../../scripts/makeELECTRONSchol.awk mappingFILEchol.txt > electronsCHOL.dat  

cp ../../../../../scripts/orderParm_defs/order_parameter_definitions_slipids_POPC_all.def ./defFILE.def

gmx trjconv -f traj.xtc -s topol.tpr -o conf.gro -dump 0

sh ../../../../../scripts/order_parameters_calculate.sh
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