Getting started in a computational chemistry lab can be challenging and, especially if you don’t have previous experience, can have a steep learning curve. But, a great part of this field is that there are thousands of people working in the same (or similar) areas, so there are a lot of resources available online. Here are a few that are useful for our lab.
Working in Linux
The computers we use in the lab all use a Linux operating system (OS) as opposed to Windows or Mac. Therefore, it’s important to become comfortable using Linux and working in a terminal, here are some useful tutorials on the subject:
Computational Chemistry
Best Practices for Foundations in Molecular Simulations
To visualize our systems or simulations, make figures, or to do some analysis, we primarily use VMD (Visual Molecular Dynamics). VMD has a lot of features and tutorials on how to use them can be found here, but if you’re just getting started, these two are good starting points:
In our lab, we run both MD simulations using both polarizable and non-polarizable force fields. For the non-polarizable, we primarily use the Amber software, which includes both the Amber MD simulation software, and several additional softwares that are very useful for preparing and analyzing your simulations (AmberTools). The Amber website is a great resource with a lot of tutorials and a very useful manual. Again, when getting started, these might be good starting points:
Finding Funding
Fellowships, scholarships, and grants are all great ways to fund your research, build your network, and improve your CV. But there is a lot of information out there and navigating it all can be difficult. Johns Hopkins has a continuously updated repository of Graduate Student and Post-doc funding opportunities that you can search through to find ones you can apply for,