Ibuprofen (IBP) 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	1289
Box size in simulations (nm)	0.8
Solvent model	TIP3P
Box type in simulations	Octahedron
MD ensemble	NVT

3D View

Download PDB + Trajectory

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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	0.85	0.85	0.86	0.85	0.86	0.86	0.86	0.86	0.87	0.86	0.87	0.87	0.87	0.87	0.88
# Exchanges	4272	4286	4283	4282	4284	4300	4339	4318	4366	4318	4322	4327	4348	4365	4391
Avg. # Exchanges	0.85	0.86	0.86	0.86	0.86	0.86	0.87	0.86	0.87	0.86	0.86	0.87	0.87	0.87	0.88

RMSd Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
RMSd_first	1.2874	0.2854
RMSd_exp	1.3470	0.2085
RMSdist_first	0.5050	0.1683
RMSdist_exp	0.5353	0.0864

RMSd Plot

Rgyr Averages

Reduced chart version

Name	Average (Å)	Standard deviation (Å)
Rgyr	3.2914	0.0656
RgyrX	3.0996	0.0829
RgyrY	1.8099	0.0356
RgyrZ	2.9630	0.0685

Rgyr Plot

Fluctuation Averages

Name	Atomic_Fluct
Average (Å)	1.0105
Standard deviation (Å)	0.3832

Atoms list

Atom name	Fluctuation (Å)
C1	0.477
C2	0.857
C3	0.557
C4	1.567
C5	1.472
C6	0.529
C7	1.324
C8	0.412
C9	1.187
C10	1.195
C11	0.606
C12	1.216
C13	1.141
O1	1.231
O2	1.386

3D View

Fluctuation Plot