Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems.
We have simulated pure liquid butane, methanol, and hydrated alanine polypeptide with the Monte Carlo technique using three kinds of random number generators (RNG's)-the standard Linear Congruential Generator (LCG), a modification of the LCG with additional randomization used in the BOSS software, and the "Mersenne Twister" generator by Matsumoto and Nishimura. While using the latter two RNG's leads to reasonably similar physical features, the LCG produces significant different results. For the pure fluids, a noticeable expansion occurs. Using the original LCG on butane yields, a molecular volume of 171.4 Å(3) per molecule compared to about 163.6-163.9 Å(3) for the other two generators, a deviation of about 5%. For methanol, the LCG produces an average volume of 86.3 Å(3) per molecule, which is about 24% higher than the 68.8-70.2 Å(3) obtained with the RNG's in BOSS and the generator by Matsumoto and Nishimura. In case of the hydrated tridecaalanine peptide, the volume and energy tend to be noticeably greater with the LCG than with the BOSS (modified LCG) RNG's. For the simulated hydrated extended conformation of tridecaalanine, the difference in volume reached about 87%. The uniformity and periodicity of the generators do not seem to play the crucial role in these phenomena. We conclude that, it is important to test a RNG's by modeling a system such as the pure liquid methanol with a well-established force field before routinely employing it in Monte Carlo simulations.
Click
Timothy H
TH
Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA.
Liu
Aibing
A
Kaminski
George A
GA
D000409:Alanine / Q000737:chemistry; D002073:Butanes / Q000737:chemistry*; D003198:Computer Simulation; D000432:Methanol / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*
D002073:Butanes; D010455:Peptides; C046888:butane; D000409:Alanine; D000432:Methanol