tools for counting ion permeation
mdtraj>=1.9.6 # 1.9.4 won't work
cd ./test/03-find_SF_from_PDB/04-NaK2K-more/
../../../count_ion.py \
-pdb em.pdb \
-xtc -xtc fix_atom_c_kpro.xtc \
-K POT -volt 300 -chunk 1000 \
-SF_seq THR VAL GLY TYR GLY > k_Cylinder_02.out
../../../count_ion_SF.py \
-pdb em.pdb \
-xtc fix_atom_c_kpro.xtc \
-K POT -volt 300 -chunk 1000 \
-SF_seq THR VAL GLY TYR GLY > k_Cylinder_03.out
conda install eigen pybind11 mdtraj numpy -c conda-forge
source gromacs2022.4_INSTALLATION_DIR/bin/GMXRC
../../../count_ion_SF_cpp.py -pdb em.pdb -xtc fix_atom_c_kpro.xtc -SF_seq THR VAL GLY TYR GLY -K POT > count_ion_SF_cpp/count.out
match_result.py \
-perm_up 02-xtck_hybrid_02/perm_up.dat \
-perm_down 02-xtck_hybrid_02/perm_down.dat \
-cylinder 03-Cylinkder/k_Cylinder_03.out > 03-Cylinkder/match02_03_03.dat