I use Packmol to create xyz file for slab-water interface, and was able to perfectly view it with jmol. However, after I insert the xyz coordinates into POSCAR file that contains the vector latices/positions and use the vtscript to create an xyz file to view the outcome, the structure obtained from packmol xyz files seems to be different. The POSCAR files seem to be distorted.
To understand what I meant, I have uploaded the POSCAR file, Packmol(xyz) file and xyz file created from the POSCAR file.
Please kindly intimate me on what I have been doing wrongly.
Looks like your lattice vectors are wrong. Look at the dotted lines in the attached--they don't match the shape of the structure. If you're not aware, ASE (https://wiki.fysik.dtu.dk/ase/) is a good program for converting file formats and looking at structures. Good luck!
Hi, If you want to create a water layer with a specific thickness please look this video, and make a specific thickness of water layer and copy-paste to your material surface. This works perfectly. My self also done MD using this method.
Video Link: https://youtu.be/qcd83uUnlGg
Hi, If you want to create a water layer with a specific thickness please look this video, and make a specific thickness of water layer and copy-paste to your material surface. This works perfectly. My self also done MD using this method.
Video Link: https://youtu.be/qcd83uUnlGg
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