MD-simulations

Prepare inputs to run equilibration and production MD simulations The steps are:

D0.1.inp D0.2.inp D0.3.inp D0.4.inp D0.5.inp D0.6.inp D0.7.inp D0.8.inp

D1.production.inp repeat with updated names to run more time.

Name		Name	Last commit message	Last commit date
Latest commit History 75 Commits
CB_RMSF.py		CB_RMSF.py
D0.1.inp		D0.1.inp
D0.2.inp		D0.2.inp
D0.3.inp		D0.3.inp
D0.4.inp		D0.4.inp
D0.5.inp		D0.5.inp
D0.7.inp		D0.7.inp
D0.8.inp		D0.8.inp
D1.production.inp		D1.production.inp
Do.6.inp		Do.6.inp
F276_lipid_distance.py		F276_lipid_distance.py
PCA.py		PCA.py
PROA_MEMB_HBONDS_pie.py		PROA_MEMB_HBONDS_pie.py
R240_LIPID_HBONDS_PLOT.py		R240_LIPID_HBONDS_PLOT.py
RAMA_traj.py		RAMA_traj.py
README.md		README.md
RG.py		RG.py
RHAMACHADRAN.py		RHAMACHADRAN.py
RHO_angles.py		RHO_angles.py
RMSD_all_CA.py		RMSD_all_CA.py
RMSD_each_TM_ieCLs.py		RMSD_each_TM_ieCLs.py
RMSF.py		RMSF.py
RMSF_sidechains.py		RMSF_sidechains.py
TM_orientaion.py		TM_orientaion.py
VectorsVSz_Axis.py		VectorsVSz_Axis.py
all_distances.py		all_distances.py
b_factor_rmsf.py		b_factor_rmsf.py
ctrbox.tcl		ctrbox.tcl
dssp.py		dssp.py
extract_force.tcl		extract_force.tcl
find_salt_bridge.py		find_salt_bridge.py
get_pdbs_for_pi_pi_dcd.py		get_pdbs_for_pi_pi_dcd.py
hbonds_pie.py		hbonds_pie.py
ligand_contacts.py		ligand_contacts.py
lipid_contacts.py		lipid_contacts.py
memb_hbonds_outputs_per_residue.py		memb_hbonds_outputs_per_residue.py
pi_pi.py		pi_pi.py
plot_RING_pipi.py		plot_RING_pipi.py
plot_RMSF.py		plot_RMSF.py
plot_memb_hbonds.py		plot_memb_hbonds.py
rhodopsin_tm_distance.py		rhodopsin_tm_distance.py
salt_bridge.py		salt_bridge.py
sort_SB.py		sort_SB.py
sum_memb_hbonds.py		sum_memb_hbonds.py
tm3_tm6.py		tm3_tm6.py
tm3_tm6_distance.py		tm3_tm6_distance.py
tm_distance_density.py		tm_distance_density.py

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