

In [19]:

    
from notebookFunctions import *
import matplotlib.pyplot as plt
%matplotlib inline
plt.rcParams['figure.figsize'] = (10,6.180)    #golden ratio
# %matplotlib notebook
%load_ext autoreload
%autoreload 2









    



The autoreload extension is already loaded. To reload it, use:
  %reload_ext autoreload

We use the data from step 3e7 to 4e7.



In [18]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/first_freeEnergy_2/rerun_1_08_Mar_154259_350-550/2d_z_qw/force_0.0/"
plot2d(location, temp=400, zmax=20)









    



<matplotlib.colors.LinearSegmentedColormap object at 0x10eafd208>

However, without any modification, just do another run.(again use step 3e7 to 4e7)



In [17]:

    
pre = "/Users/weilu/Research/server/feb_2018/week_of_feb19"
location = pre + "/freeEnergy_rg_0.1_lipid_1.0_mem_1_2/rg_0.1_lipid_1.0_mem_1_350-550/2d_z_qw/force_0.0/"
plot2d(location, temp=500, zmax=30)









    



<matplotlib.colors.LinearSegmentedColormap object at 0x10eafd208>



In [13]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week/"
location = pre + "/abs_first_freeEnergy_-1/rerun_2_10_Mar_183455_400-500/2d_z_qw/force_0.0/"
plot2d(location, temp=500, zmax=20)









    



<matplotlib.colors.LinearSegmentedColormap object at 0x10eafd208>



In [ ]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week/"
location = pre + "/abs_first_freeEnergy_-1/rerun_2_10_Mar_183455_400-500/2d_z_qw/force_0.0/"
plot2d(location, temp=500, zmax=20)

So I went back to first run, and continue the simulation. using step 4e7 to 5e7.(and 5e7 to 6e7)



In [4]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/first_freeEnergy_3/rerun_2_09_Mar_154823_350-550/2d_z_qw/force_0.0/"
temp =400
location1 = location + f"pmf-{temp}.dat"
location = pre + "/first_freeEnergy_4/rerun_2_09_Mar_154823_350-550/2d_z_qw/force_0.0/"
location2 = location + f"pmf-{temp}.dat"
plot2d_side_by_side(location1, location2)

second run, with step 4e7 to 5e7(and 5e7 to 6e7)



In [5]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/freeEnergy_3/rerun_2_06_Mar_225059_350-550/2d_z_qw/force_0.0/"
temp =400
location1 = location + f"pmf-{temp}.dat"
location = pre + "/freeEnergy_4/rerun_2_06_Mar_225059_350-550/2d_z_qw/force_0.0/"
location2 = location + f"pmf-{temp}.dat"
plot2d_side_by_side(location1, location2)

So I have to conclude that the initial figure is not valid.

However, If I pick the average z of helix 6 as RC



In [11]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/z_6_freeEnergy_-1/rerun_2_10_Mar_183455_400-500/2d_z_qw/force_0.0/"
temp = 490
location1 = location + f"pmf-{temp}.dat"
pre = "/Users/weilu/Research/server/mar_2018/03_week"
location = pre + "/second_z_6_freeEnergy_-1/rerun_2_11_Mar_160738_400-500/2d_z_qw/force_0.0/"
location2 = location + f"pmf-{temp}.dat"
plot2d_side_by_side(location1, location2, zmax=30)



In [7]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/z_6_freeEnergy_-1/rerun_2_10_Mar_183455_400-500/2d_z_qw/force_0.0/"
temp =500
location1 = location + f"pmf-{temp}.dat"
pre = "/Users/weilu/Research/server/mar_2018/03_week"
location = pre + "/second_z_6_freeEnergy_-1/rerun_2_11_Mar_160738_400-500/2d_z_qw/force_0.0/"
location2 = location + f"pmf-{temp}.dat"
plot2d_side_by_side(location1, location2, zmax=30)



In [8]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/first_freeEnergy_3/rerun_2_09_Mar_154823_350-550/2d_z_qw/force_0.0/"
temp =500
location1 = location + f"pmf-{temp}.dat"
location = pre + "/first_freeEnergy_4/rerun_2_09_Mar_154823_350-550/2d_z_qw/force_0.0/"
location2 = location + f"pmf-{temp}.dat"
plot2d_side_by_side(location1, location2)



In [9]:

    
pre = "/Users/weilu/Research/server/mar_2018/02_week"
location = pre + "/freeEnergy_3/rerun_2_06_Mar_225059_350-550/2d_z_qw/force_0.0/"
temp =500
location1 = location + f"pmf-{temp}.dat"
location = pre + "/freeEnergy_4/rerun_2_06_Mar_225059_350-550/2d_z_qw/force_0.0/"
location2 = location + f"pmf-{temp}.dat"
plot2d_side_by_side(location1, location2)



In [ ]: