Journal of Physical Chemistry B, Vol.116, No.1, 469-475, 2012
Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results
The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities compare satisfactorily well with very recently published experimental data on equivalent systems. In particular, alpha conformation-probabilities for all of the dipeptides remain much lower than either beta or PR propensities. This result is in agreement with most experimental data for dipeptides. However, it is also in contrast with most simulation studies performed so far with other force fields, where alpha conformations result even more probable than P(II) or beta ones. We discuss the behavior of the OPLS-AA force field, which can be useful for the improvement of this model in reproducing the recent experimental observations on amino acid dipeptides.