I have cut the amorphous model into cylindrical pores and thereafter I have saturated all the dangling bonds with hydrogen and -OH groups.
Now I have to optimize the geometry of the structure. How it can be done?
If you just need to do a quick and dirty optimization to make sure the structure is reasonable, I would use GULP (the general utility lattice program). If you don't have GULP, you can request it at the following website: https://nanochemistry.curtin.edu.au/gulp/request.cfm?rel=download. If you actually need to do a full energy minimization (the most stable geometry possible with the network of atoms you've modeled), you need to use an ab initio code like VASP or GAUSSIAN.
Dear Hummer, I have XYZ file of amorphous silica with only co-ordinates of the structure. Is it possible to optimize the structure with this xyz co-ordinate file only. or dihedral angle and other information required too?
Hi,
Which Molecular dynamics program do you want to use after geometry optimization?
And which forcefield do you want to use?
i have developed my own code using monte carlo in grand canonical ensemble. so before that i hv to optimize geometry of the molecule after cutting ....
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