(LHN) 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	49
Molecule charge (simulated)	0
System number of atoms	2878
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	0.87	0.86	0.86	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87
# Exchanges	4323	4355	4315	4357	4346	4375	4352	4334	4359	4356	4338	4328	4369	4354	4374
Avg. # Exchanges	0.86	0.87	0.86	0.87	0.87	0.88	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87	0.87

RMSd Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
RMSd_first	1.1072	0.4498
RMSd_exp	0.8825	0.3067
RMSdist_first	0.5607	0.3224
RMSdist_exp	0.4884	0.2571

RMSd Plot

Rgyr Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
Rgyr	4.9652	0.1465
RgyrX	3.5905	0.1357
RgyrY	3.7742	0.0824
RgyrZ	4.7079	0.1512

Rgyr Plot

Fluctuation Averages

Name	Atomic_Fluct
Average (Å)	0.7102
Standard deviation (Å)	0.4202

Atoms list

Atom name	Fluctuation (Å)
N1	0.423
N3	0.395
C4	0.38
C5	0.525
C6	0.782
C7	0.735
C8	0.42
C10	0.428
C13	0.712
C15	0.349
C17	0.601
C21	0.562
C22	1.049
C24	1.979
C23	1.999
N4	0.819
O2	1.556
C16	0.384
C18	0.831
C19	0.734
C3	0.475
O1	0.739
C2	0.321
C1	0.503
N2	0.704
C9	0.245
C14	0.57
C12	0.576
F2	0.857
C11	0.521
F1	0.841

3D View

Fluctuation Plot