GROMACS version: 2021.4
GROMACS modification: Yes/No
Currently, I am doing an MD simulation to study the effect on the surface wettability of DES on SiO2-based surfaces. I used an OPLS-AA force-field and Nose-Hoover thermostat at 300K in the NVT ensemble. Pairwise electrostatics cut off at 1.2 nm, with a particle mesh Ewald (PME) treatment of long-range interactions.
Problem: The solvent molecules (DES) are stuck or frozen throughout the simulation. i.e., No movement of DES molecules on the SiO2 surface.
I tried many times to sort out the problem but failed. Does anyone have any experience with this system?
I really appreciate any help you can provide.
…Bappaditya
Your DES molecules don’t “freeze” – they get adsorbed. What is the SiO2 model you’re using?
Thank you for your reply.
The structure of the Sio2 model is simply generated from VMD.
In VMD, I use the “Inorganicbuilder” plugin.
…bappaditya
This “simply generated” is the issue. The topologies used by inorganicbuilder are likely garbage, so one needs to use existing literature to:
a) understand what degree of adsorption is expected on silica surface and what surface it is (crystalline or amorphous).
b) adjust partial charges and LJ parameters according to published data, etc.
Also, keep in mind that silica surface carries pH-dependent surface charge.
Here the silica surface is crystalline. All parameter values are taken from Published articles.
The integration failed during the simulations, and all the molecules (solvent) in the box stopped moving, which does not happen on the graphite surface.