Hello everyone,
I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to generate the initial atomic structure of the system. The "nanomaterial modeler" module in CHARMM-GUI comes in handy creating the atomic structure. But I do not have complete control over my structure if I use it. I need to attach the hydroxyl groups to the dangling silicon atoms in the interface as well. Therefore, it feels a bit complicated when defining the bonds and angles in the system using Matlab or python. As I'm using CHARMM potential, the relevant potential parameters need to be specified as well in the atomic data file. Any advice would be highly appreciated.
This is the system I could generate from CHARMM-GUI,
To generate an initial atomic structure of a silica-water system, there are several approaches that can be used. One popular approach is to use a software package like Materials Studio or Avogadro, which has built-in tools for generating molecular structures. Here are the steps you can follow:
Note that the process of generating an atomic structure can be time-consuming and require some trial and error. However, by following the steps outlined above and with some experimentation, you should be able to create a reliable structure for your silica-water system.
Satyendra Singh Thank you very much for your reply. I'm looking at the VMD and the topotools plugin right now. Really appriciate your suggestions.
Hi,
For the initial model you can use packmol.
https://m3g.github.io/packmol/
As water force field is already available in the VMD. You only need Silica force field parameter.
For the silica you can use CgenFF or ligapargen or either use any force field that suits you.
In ligpargen you have flexibility to choose Charmm, Gromacs, OPLS-AA etc. force field parameter.
Regards,
Aashish
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