D-[(n-hydroxyamino)carbonyl]phenylalanine (INF) 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 27
Molecule charge (simulated) -1
System number of atoms 1029
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 0.83 0.83 0.83 0.84 0.84 0.84 0.84 0.85 0.84 0.85 0.85 0.85 0.85 0.85 0.86
# Exchanges 4108 4141 4192 4198 4203 4182 4245 4215 4166 4262 4223 4236 4280 4212 4275
Avg. # Exchanges 0.82 0.83 0.84 0.84 0.84 0.84 0.85 0.84 0.83 0.85 0.84 0.85 0.86 0.84 0.86
RMSd Averages
Reduced chart version
Name Average (Å) Standard deviation (Å)
RMSd_first 1.3960 0.3698
RMSd_exp 1.4262 0.3992
RMSdist_first 0.7339 0.3143
RMSdist_exp 0.7262 0.1917
RMSd Plot
Rgyr Averages
Reduced chart version
Name Average (Å) Standard deviation (Å)
Rgyr 2.9766 0.1371
RgyrX 2.5450 0.1227
RgyrY 2.3528 0.2603
RgyrZ 2.3769 0.1102
Rgyr Plot
Fluctuation Averages
Name Atomic_Fluct
Average (Å) 1.0171
Standard deviation (Å) 0.3728
Atoms list
Atom name Fluctuation (Å)
N 0.415
CA 0.562
C 0.682
O 1.303
CB 1.293
CG 0.489
CD1 1.194
CD2 1.274
CE1 1.414
CE2 1.529
CZ 1.237
OXT 1.391
C1 0.489
N2 0.812
O1 0.911
O2 1.278
3D View
Fluctuation Plot