Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory
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The goal of the present study is to ascertain the differential performance of a long molecular dynamics trajectory versus several shorter ones starting from different points in the phase space and covering the same sampling time. For this purpose we have selected the 16-mer peptide Bak16BH3 as model of study and carried out several samplings in explicit solvent. Samplings include a 8 us trajectory (sampling S1); two 4 us (sampling S2); four 2 us (sampling S3); eight 1 =s (sampling S4); sixteen 0.5 us (sampling S5) and eighty 0.1 us (sampling S6). Moreover, the 8 =s trajectory was further extended to 16 us to have reference values of the diverse properties measured. The diverse samplings were compared qualitatively and quantitatively. Among the former, we carried out a comparison of the conformational profile of the peptide using cluster analysis. Moreover, we also got insight into the interchange among these structures along the sampling process. Among the latter, we have computed the number of new conformational patterns sampled with time, using strings defined from the conformations attained by each of the residues in the peptide. We also compared the location and depth of the free energy surface minima obtained using a Principal Component Analysis. Finally, we also compared the helical profile per residue at the end of the sampling process. Results suggest that a few short molecular dynamics trajectories may provide a better sampling than one unique trajectory. Moreover, this procedure can also be advantageous to avoid getting trapped in a local minimum. However, caution should be exercised since short trajectories need to be long enough to overcome local barriers surrounding the starting point and the required sampling time depends on the number of degrees of freedom of the system under study. An effective way to get insight into the minimum MD trajectory length requires monitoring the convergence of different structural features as shown in the present work.
CitationPerez, J., Tomas, M., Rubio, J. Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory. "Journal of chemical information and computer sciences", 1 Octubre 2016, vol. 56, núm. 10, p. 1950-1962.