Cocaine (COC) 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	44
Molecule charge (simulated)	1
System number of atoms	1682
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	0.87	0.87	0.87	0.87	0.87	0.87	0.88	0.88	0.88	0.88	0.88	0.88	0.89	0.89	0.89
# Exchanges	4314	4341	4372	4337	4374	4361	4358	4403	4447	4412	4400	4360	4439	4418	4428
Avg. # Exchanges	0.86	0.87	0.87	0.87	0.87	0.87	0.87	0.88	0.89	0.88	0.88	0.87	0.89	0.88	0.89

RMSd Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
RMSd_first	0.8262	0.3186
RMSd_exp	0.8324	0.3050
RMSdist_first	0.4423	0.1655
RMSdist_exp	0.4323	0.1552

RMSd Plot

Rgyr Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
Rgyr	3.4720	0.0593
RgyrX	3.2240	0.0635
RgyrY	2.8104	0.1019
RgyrZ	2.4099	0.0394

Rgyr Plot

Fluctuation Averages

Name	Atomic_Fluct
Average (Å)	0.5378
Standard deviation (Å)	0.3752

Atoms list

Atom name	Fluctuation (Å)
C1	0.72
O5	0.567
C6	0.277
O7	0.496
C8	0.229
C10	0.174
N12	0.194
C14	0.389
C18	0.259
C21	0.285
C24	0.252
C26	0.341
C29	0.311
O1	0.433
C2	0.354
O3	0.995
C4	0.197
C5	1.26
C7	1.28
C9	0.433
C11	1.21
C13	1.176

3D View

Fluctuation Plot