Hi,
I am performing MD simulations of ZnO nanocluster. I created nanocluster in Material Studio but atoms are not arranged. Can any1 help me to arrange the atoms in PDB file using CrystalMaker software. Please find the attached PDB of ZnO.
Thanks a lot.
Hi Faez,
Find attached the PDB file for ZnO nanocluster with the atoms arranged using CrystalMaker.
Hi
I am glad that you got the file you needed, but can I ask a question? Why did you need an arranged file at the first place?
Also, double check the spacing between columns of pdb file when you get them from material studio. I found it quiet different from the standard of the pdb and this will cause lots of problem. For example in one occasion the x coordinate of all atoms was started one column sooner than its standard. When you visualize that in vmd all atoms are very close to each other, as the values after decimal points have been detected only. When you do the simulation with (GROMACS e.g.) other softwares, you get a very high energy structure following by a quick crash of the simulation.
Good luck
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics