Cholic acid (CHD) 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	68
Molecule charge (simulated)	-1
System number of atoms	2114
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	0.81	0.81	0.81	0.82	0.82	0.82	0.82	0.83	0.83	0.83	0.84	0.84	0.84	0.84	0.85
# Exchanges	4058	4107	4058	4142	4076	4108	4121	4159	4144	4184	4223	4172	4174	4205	4258
Avg. # Exchanges	0.81	0.82	0.81	0.83	0.82	0.82	0.82	0.83	0.83	0.84	0.84	0.83	0.83	0.84	0.85

RMSd Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
RMSd_first	0.8987	0.1878
RMSd_exp	0.8509	0.1403
RMSdist_first	0.3677	0.0700
RMSdist_exp	0.5213	0.1093

RMSd Plot

Rgyr Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
Rgyr	4.4075	0.0980
RgyrX	3.9823	0.1004
RgyrY	2.4255	0.0180
RgyrZ	4.1361	0.1106

Rgyr Plot

Fluctuation Averages

Name	Atomic_Fluct
Average (Å)	0.4400
Standard deviation (Å)	0.3066

Atoms list

Atom name	Fluctuation (Å)
C1	0.245
C2	0.311
C3	0.382
O3	0.538
C4	0.311
C5	0.226
C6	0.222
C7	0.188
O7	0.297
C8	0.163
C9	0.131
C10	0.168
C11	0.235
C12	0.317
O12	0.41
C13	0.318
C14	0.263
C15	0.351
C16	0.456
C17	0.43
C18	0.372
C19	0.302
C20	0.537
C21	0.646
C22	0.664
C23	0.776
O25	1.375
C24	0.734
O26	1.392

3D View

Fluctuation Plot