ncolumns=len(line.split())
if ncolumns==14:
- x,y,s,r,ek,rms= np.loadtxt('remd_all.stat',usecols=(11,3,0,13,2,5),unpack=True)
+ x,y,s,r,ek,rms= np.loadtxt('remd_all.stat',usecols=(11,3,1,13,2,5),unpack=True)
+ x0,s0,r0,rms0= np.loadtxt('remd_all0.stat',usecols=(11,1,13,5),unpack=True)
else:
- x,y,s,r= np.loadtxt('remd_all.stat',usecols=(7,3,0,9),unpack=True)
+ x,y,s,r= np.loadtxt('remd_all.stat',usecols=(7,3,1,9),unpack=True)
+ x0,s0,r0= np.loadtxt('remd_all0.stat',usecols=(7,1,9),unpack=True)
+s=s*0.0489
+s0=s0*0.0489
hall,binall=np.histogram(y,bins=40,density=False)
plt.xlim(min(binall), max(binall[hall>4]))
-plt.ylim(0,max(hall)/4)
+#plt.ylim(0,max(hall)/4)
plt.ylabel('number of samples')
plt.xlabel('potential energy [kcal/mol]')
colors = cm.rainbow(np.linspace(0, 1, len(Tremd)))
for T,c in zip(Tremd,colors):
yt=y[x==T]
- h,bin=np.histogram(yt,bins=40,density=False)
+ h,bin=np.histogram(yt,bins=40,range=(min(binall),max(binall[hall>4])),density=False)
center = (bin[:-1] + bin[1:]) / 2
plt.plot(center,h,'-',color=c)
# plt.bar(bin[:-1], h, width = bin[2]-bin[1],color=c)
plt.clf()
plt.ylabel('bath temperature [K]')
-plt.xlabel('step*replica')
+plt.xlabel('time*replica')
-replica=range(len(Tremd))
+replica=range(int(sys.argv[2]))
+#colors = cm.rainbow(np.linspace(0, 1, len(replica)))
+cmap = plt.get_cmap('hot')
+colors = cmap(np.linspace(0, 1, len(replica)*1.4))
for i,c in zip(replica,colors):
- yt=x[r==i]
- xt=(s+r*max(s))[r==i]
+ yt=x0[r0==i]
+ xt=(s0+r0*max(s0))[r0==i]
plt.plot(xt,yt,'-',color=c)
plt.savefig('remd_ex.png')
+colors = cm.rainbow(np.linspace(0, 1, len(Tremd)))
if ncolumns==14:
plt.clf()
plt.savefig('remd_ene_rms.png')
+ plt.clf()
+ plt.xlabel('time*replica')
+ plt.ylabel('rmsd')
+ for i in replica:
+ yt=rms0[r0==i]
+ xt=(s0+r0*max(s0))[r0==i]
+ tt=x0[r0==i]
+ plt.scatter(xt,yt,c=tt,edgecolors='face',s=0.1,cmap=cm.rainbow,vmin=Tremd[0],vmax=Tremd[-1])
+ plt.xlim(0,max(s)+max(s)*max(r))
+ plt.ylim(bottom=0)
+ plt.savefig('remd_step_rms.png')
x,y,rms= np.loadtxt('file_wham.thermal',usecols=(0,6,4),unpack=True)
plt.clf()
plt.xlabel('bath temperature [K]')
plt.ylabel('heat capacity')
-plt.xlim(Tremd[1]-10, Tremd[-1]+10)
+plt.xlim(Tremd[0]-10, Tremd[-1]+10)
plt.plot(x,y,'-',color=c)
plt.savefig('remd_cv.png')
plt.clf()
plt.xlabel('bath temperature [K]')
plt.ylabel('average RMSD')
- plt.xlim(Tremd[1]-10, Tremd[-1]+10)
+ plt.xlim(Tremd[0]-10, Tremd[-1]+10)
plt.plot(x,rms,'-')
plt.savefig('remd_rmsd.png')
+