13-cyclohexyl-3-methoxy-17,22-dimethyl-7h-10,6-(methanoiminothioiminobutanoiminomethano)indolo[2,1-a][2]benzazepine-14,23-dione 16,16-dioxide (0LN) Summary

METADATA
Parameter Value
Method HamiltonianREMD
Number of MD replicas 16
Length of the MD simulations (ns) 10
Number of steps between exchanges 100
Force Field General Amber Force Field (GAFF)
Charge scheme Semi-Empirical (AM1)
REMD Progression Geometric Progression
Initial (low) temperature (K) / Scaling factor 298 / 1
Final (high) temperature (K) / Scaling factor 498 / 0.59
Molecule number of atoms 80
Molecule charge (simulated) 0
System number of atoms 2498
Box size in simulations (nm) 0.8
Solvent model TIP3P
Box type in simulations Octahedron
MD ensemble NVT
0
1-2 2-3 3-4 4-5 5-6 6-7 7-8 8-9 9-10 10-11 11-12 12-13 13-14 14-15 15-16
Probabilities 0.81 0.82 0.82 0.82 0.82 0.83 0.82 0.83 0.83 0.83 0.84 0.84 0.84 0.85 0.84
# Exchanges 4026 4137 4117 4141 4089 4151 4097 4147 4158 4156 4206 4202 4248 4228 4173
Avg. # Exchanges 0.81 0.83 0.82 0.83 0.82 0.83 0.82 0.83 0.83 0.83 0.84 0.84 0.85 0.85 0.83
RMSd Averages
Reduced chart version
Name Average (Å) Standard deviation (Å)
RMSd_first 1.3058 0.1746
RMSd_exp 0.9745 0.1129
RMSdist_first 0.7830 0.0909
RMSdist_exp 0.5077 0.0630
RMSd Plot
Rgyr Averages
Reduced chart version
Name Average (Å) Standard deviation (Å)
Rgyr 4.9273 0.0552
RgyrX 4.0435 0.0498
RgyrY 4.7511 0.0658
RgyrZ 3.1035 0.0502
Rgyr Plot
Fluctuation Averages
Name Atomic_Fluct
Average (Å) 0.4028
Standard deviation (Å) 0.2204
Atoms list
Atom name Fluctuation (Å)
O36 0.94
C34 0.422
N35 0.357
C38 0.784
C37 0.62
C39 0.733
C40 0.768
C41 0.564
N31 0.388
C42 0.676
S30 0.258
O32 0.519
O33 0.444
N29 0.285
C27 0.309
O28 0.588
C1 0.264
C19 0.278
C20 0.282
N9 0.249
C5 0.237
C6 0.274
C18 0.249
C17 0.184
C24 0.241
C23 0.276
O25 0.428
C26 1.147
C22 0.274
C21 0.228
C16 0.176
C8 0.205
C7 0.187
C4 0.21
C3 0.256
C2 0.279
C10 0.201
C15 0.307
C14 0.455
C13 0.522
C12 0.49
C11 0.364
3D View
Fluctuation Plot