I am looking at building/buying myself a workstation for scientific computing. I will be doing molecular dynamics simulations that are memory intensive (data on a large number of particles and a million time steps or more) and require multiple instances of the same code running (to generate an ensemble). I am new to computing but my guess is I will be using C++ and learn to utilize the best memory handling practices. In terms of ensemble averaging, it appears to me I could either just run the code N times or maybe run N instances of the codes in simultaneously on N processors. At this point I don't have access to HPC resources and I am only trying to get a simple desktop (maybe 2 or 4 cores) but I want to learn to make this code parallel. 

At this point I know very little about the code itself to make a more specific assessment of my needs. However, my question is what might be the very essential features I should keep in mind while buying a workstation. For example, things to keep in mind if eventually I want to transition to HPC, things to keep in mind if some amount of parallel processing needs to be done (or just having 2 or more cores in enough) etc.