GROMACS version: 2020.6
GROMACS modification: No
In order to simulate the gas adsorption on MOF, a rectangular box was set up, and when its length was larger, the molecules in the gas region appeared to be agglomerated, at a temperature of 298 K, with different force fields and lower pressures. What could be the cause of this?
What type of molecules make up the gas and what is the density?
The gas molecules are all carbon dioxide, and the gas-phase density in the first graph is about 9 kg/m^3 under 0.4 MPa. The density distribution along the length is shown in the figure:
Where did you get the parameters for CO2?
I obtained the CO2 parameters from the following paper:
https://doi.org/10.1021/acs.jctc.9b00653
The above also occurred with the TraPPE force field from http://trappe.oit.umn.edu/, as soon as the box reached a certain length.
There is no above mentioned problem as long as the box is shorter, so this doesn’t seem to be due to the force field. Does a box that is too long in GROMACS increase the numerical error?
Moreover, this abnormal aggregation occurs mainly at the two ends of the box, and the middle near the MOF is normal.
How long is long? And what thermostat are you using with what coupling time? If your box is very long and use a thermostat, atoms with small coordinates will get colder and those with large coordinates hotter than the reference temperature.
Generally the above situation occurs for lengths longer than 200 nm, using a V-rescale thermostat with the time constant set to 0.2 ps and the temperature set to 298K.
With a box larger than 200 nm the effects of rounding errors on the coordinates are quite large. But then I would only expect condensation for small coordinate values, not large ones. Where is the origin of the simultation in the two plots you shows in your first post?
Their origins are both on the left boundaries.
The mdp file for the pre-equilibrium simulation are shown below:
eq.mdp (744 Bytes)
The molecular aggregation process is shown below:
Why does the MOF move (fast) initially?
I can’t easily see from this animation, but could it be that all droplets nucleate on the left side of the box? Then this could be explained by the rouding issues.
The box size changes rapidly during the non-equilibrium process of controlled pressure and temperature. The MOF moves due to the fixed center of mass, which is always at the center of the box, and so moves with the change in box size.
Droplets form on both the left and right sides of the box.
Is the rapid change in box size a possible reason?
I guess that can be a possible reason. I don’t know that the timescale of the movie is, but the change in box size seems very rapid. Try increasing tau_p and see if the issue goes away.
Thank you for your answers, the gas adsorption results of MOF are reliable despite some artificial factors causing molecular aggregation.