6-o-cyclohexylmethyl guanine (CMG) 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	35
Molecule charge (simulated)	0
System number of atoms	1508
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	0.88	0.88	0.88	0.88	0.88	0.89	0.89	0.89	0.89	0.89	0.90	0.90	0.90	0.90
# Exchanges	4344	4419	4399	4392	4412	4378	4443	4477	4491	4464	4445	4537	4496	4500	4546
Avg. # Exchanges	0.87	0.88	0.88	0.88	0.88	0.88	0.89	0.90	0.90	0.89	0.89	0.91	0.90	0.90	0.91

RMSd Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
RMSd_first	1.0414	0.3124
RMSd_exp	0.9484	0.3049
RMSdist_first	0.4635	0.1620
RMSdist_exp	0.4284	0.2167

RMSd Plot

Rgyr Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
Rgyr	3.4722	0.1352
RgyrX	3.1434	0.1529
RgyrY	2.8048	0.1008
RgyrZ	2.5222	0.0830

Rgyr Plot

Fluctuation Averages

Name	Atomic_Fluct
Average (Å)	0.7115
Standard deviation (Å)	0.3920

Atoms list

Atom name	Fluctuation (Å)
N1	0.426
C2	0.324
N3	0.406
C4	0.307
C5	0.242
C6	0.415
O6	0.751
C9	0.953
N7	0.419
C8	0.529
N9	0.571
N2	0.54
C10	0.563
C11	1.327
C12	1.393
C13	0.938
C14	1.405
C15	1.298

3D View

Fluctuation Plot