Hi all,
i am currently working on montmorillonite clay. i am using Gromacs, clayff and vmd. i got a unit cell from an online data base but would like to create up to 6 or 16 unit cell model. also i want to create itp file for the model. any form of suggestion would be appreciated.
Gromacs works very well for the systems that included protein, DNA and lipids. Gromacs database is also developed (force field parameters, bonded, non-bonded interaction) for these type of molecules. If you would like to introduce other type of molecules you have to introduce all necessary parameters to the Gromacs.
My first concern is: what kind of molecules present in your system? Gromacs generates topology files for the above indicated molecules. If your system contain other kind of molecules, you have to create .itp file and indicate it in the topology.
Note that, it is not only creating itp file but you also have to indicate correct force field parameters as well.
Hello, is there any sources, tutorial or guideline that can help me to build montmorillonite model using GROMACS?
Appreciate your help.
My quirky matlab scripts do just that. It comes with some simple examples/tutorials:
https://www.mathworks.com/matlabcentral/fileexchange/59622-atom
- Badges
- Science topic