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

3D View

Download PDB + Trajectory

0

REMD stats

Open Replica Exchange chart

	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