D-[(n-hydroxyamino)carbonyl]phenylalanine (INF) Summary
TRAJECTORIES
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 |
REMD stats
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
