What programming language do you use ? what sort of proteins ? a little background will give your question more context. Is the problem simulating the proteins or understanding the technique ?
The problem about simulating the pehaviour of membrane proteins, specially understanding the mechanism by which the membrane protein maintains its job, we are concentrate to understant the mechanism of one of the most important protein that embeded in the cell membrane (Na,K-ATPase), we already did sort of laboratory experiments and we need those programs to simulate the results we have,