Computational chemistry is a discipline that concerns the computing of physical and chemical properties of atoms and molecules using the fundamentals of quantum mechanics. The expense of computational chemistry calculations is significant and limited by available computational capabilities. The use of high-performance computing clusters alleviate such calculations. However, as high-performance computing (HPC) clusters have always required a balance between four major factors: raw computing power, memory size, I/O capacity, and communication capacity. In this paper, we present the results of standard HPC benchmarks in order to help assess the performance characteristics of the various hardware and software components of a home-built commodity-class Linux cluster. We optimized a range of TCP/MPICH parameters and achieved a maximum MPICH bandwidth of 666 Mbps. The bandwidth and latency of GA put/get operations were better than the corresponding MPICH send/receive ones. We also examined the NFS, PVFS2, and Lustre parallel filesystems and Lustre provided the best read/write bandwidths with more than 90% of those of the local filesystem.