Hi Dear researchers
I have some questions
I wanna drawing/model a nanoparticle with a computational method. I know some tools for drawing nanoparticle such as (Material studio, Avogadro, Gaussview and VESTA). But I don’t know which software is better. please recommend and introduce a good software.
After I had successfully drawn a nanoparticle i have a new problem. I don’t know how get force field parameter for a MD simulation (via gromacs package).
hello
Gaussview and these different programs can not do any thing in molecular dynamic.
i think that you can do anything in this moment. you read the molecular dynamic basis rules.
thank you all
Dr.Amanda Barnard suggested that
Milad Baghery,
1. All packages have different capabilities. Try them and see which one you like.
2. Read the literature. Petiole publish their parameters.
3. Google them. People post these or place them in supplementary information if their papers.
4. Do a PhD is computational chemistry. It takes years to learn these techniques properly.
Regards,
-Amanda Barnard
Hi Milad,
Unfortunately, there are no simple answers to your questions. The "best" software, force field, and simulation package will depend on exactly what you are trying to do.
For building your model, Discover Studio, UCSF Chimera, or VMD are all free and publicly available.
Force field parameters will depend on exactly what your nanoparticle is. For some nanoparticles there are no force field parameters. For that you will have to Google "Force field parameterization" and develop your own, or collaborate with someone who can develop them.
Hope that helps.
Kind regards,
Andrew
Dear Milad,
I am also working on the nanoparticle dynamics. Before answering to your question, let me remind you that the behaviour and chemistry of nanoparticle is very very different from the molecular systems as they are closely packed (solid state) and dominated by their surfaces. We therefore for such system usually takes special care for the surfaces (miller/weiss indices) and unit cell it forms in general. Also, as per my opinion, the dynamic behaviour for such system cannot be modelled accurately by the packages that are built for the molecular systems (like Gaussian etc.). Now, coming back to the force field specification and atomic parameterization (atom types), it is very crucial for accurate solving of the forces via Newtons equations of motion.
I, therefore, suggest you read more and more literature and try to figure out what sort of metal it is and what others have done for the same.
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