Contents
Analysis
Simulation of each DISTANCE gives a separate pullf and pullx data. A plot of a pullx data and histogram of all pullx data is shown below:
Fig.3: (Top) position v/s time when DISTANCE = 3nm, (Bottom) Histogram of the position
gmx analyze is used to obtain the average position and average distance for each simulation.
Fig.4: Mean force between colloids along distance shows the depletion force of colloids when they come close to each other enough
Discussion
comparison between ionic water and pure water:
Both in presence or absence of ion, the molecules tend to collide with each other. There is a strong force of attraction when the molecules are very close i.e surface of the molecules are only 0.4 nm apart. In presence of ion the force of attraction is low compared to when there is no ion.
Repulsion when colloid comes together:
As the distance between particle reduces less than about 1.7 nm the attractive force reduces and for much lower distances the forces are repulsive for both with ion and without ion.
Periodic attraction and repulsion:
A periodic attraction and repulsion can be observed within a distance of 0.25 nm i.e of the size of a water molecule. It implies that a non-integer no. of water molecule is not favorable. Also, for system with ion the periodic distance is different implying the interference of ion in the water layer.
Spring Constant
Fig.5: When two colloids are close enough, the attraction force between colloids overpowers the spring pulling force. In this manner, colloid cannot hold its original position
The spring is not very stiff to maintain the position of the particle, and hence there is a sudden jump that can be observed when particles are about 1.8 nm apart as shown in the video:
Fig. 6: The spring like pulling force can no longer hold its place
spring constant matters
If the spring constant is too strong, the force derived might be very small to identify from noises. On the other hand, if the spring constant is too weak, it cannot hold the colloid particle firm enough, and we cannot further analyze the potential since the position shifted a lot. Despite trial and error, spring constant can be estimated from the following equation:
k_spring=kb*T/σ2
pull options matter
There are several possible ways to specify the position of colloids with pull features in mdp options. However “distance” for pull-coord-geometry option will give the the distance of particles deviates from initial point instead of relative position. In this manner, the calculated potential will be higher than what it actually is. With “distance-periodic” for pull-coord-geometry, the problem could be corrected.
******tar file here !********