Tosyl-d-proline (TPR) 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	32
Molecule charge (simulated)	-1
System number of atoms	1358
Box size in simulations (nm)	0.8
Solvent model	TIP3P
Box type in simulations	Octahedron
MD ensemble	NVT

3D View

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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	0.84	0.83	0.84	0.85	0.85	0.85	0.85	0.86	0.85	0.85	0.86	0.86	0.87	0.87
# Exchanges	4196	4150	4143	4218	4203	4243	4231	4272	4298	4284	4275	4260	4256	4345	4359
Avg. # Exchanges	0.84	0.83	0.83	0.84	0.84	0.85	0.85	0.85	0.86	0.86	0.86	0.85	0.85	0.87	0.87

RMSd Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
RMSd_first	1.0315	0.5485
RMSd_exp	1.1157	0.5109
RMSdist_first	0.4127	0.2834
RMSdist_exp	0.4883	0.2927

RMSd Plot

Rgyr Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
Rgyr	3.0952	0.0827
RgyrX	2.8361	0.0924
RgyrY	1.5880	0.0959
RgyrZ	2.9275	0.1440

Rgyr Plot

Fluctuation Averages

Name	Atomic_Fluct
Average (Å)	0.9227
Standard deviation (Å)	0.4279

Atoms list

Atom name	Fluctuation (Å)
C1	1.244
C2	0.523
C3	1.213
C4	1.175
C5	0.21
C6	1.196
C7	0.844
S8	0.49
O9	0.783
O10	0.736
N	0.459
CD	1.225
CG	1.072
CB	0.49
CA	0.447
C	1.045
O	1.748
OXT	1.708

3D View

Fluctuation Plot