Dear Experts,
I am currently conducting a Molecular Dynamics (MD) simulation using the NAMD package to observe the formation of a two-phase system between glucose, acetonitrile, and water. To provide more detail, my system comprises 3930 atoms, which include 80 glucose molecules, 250 acetonitrile molecules, and 170 TIP3P water molecules.
We have already conducted experimental work on this system and are now seeking to corroborate those findings with a theoretical approach. However, after 8ns of simulation, the molecules merely move and interact with each other without forming the anticipated two-phase system.
(Additional parameters used in the simulation include Periodic Boundary Conditions (PBC) and the CHARMM force field @ NPT ensemble.)
Hello
8 ns might not be sufficient time for the system to reach equilibrium and undergo phase separation, especially for a system with a relatively large number of molecules. Phase separation is a collective phenomenon that typically requires longer simulation times to observe.
The system size you described (3930 atoms) may be too small to observe phase separation, especially if the system is highly miscible or if there are strong interactions between the components.
Some Suggestions:
Increase Simulation Time, Explore Alternative Force Fields, Increase System Size.
If it is possible you can compare your simulation results with available experimental data, such as phase diagrams, densities, or other relevant thermodynamic properties, to assess the accuracy of your model and identify potential discrepancies.
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