You are here: HomeResearch topicsComputational biochemistry and soft matterLine 3 highlightsLine 3 highlights 2016Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory

Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory

J. J. Pérez, M. S. Tomas, J. Rubio-Martínez.

J. Chem. Inf. Model., 56 (2016) 1950.

Mostreig de l’espai configuracional amb múltiples trajectòries

 

In this work we did an extensive study 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 selected the Bak16BH3 peptide as model of study and carried out several samplings in explicit solvent. Samplings include a 8 μs trajectory; two 4 μs; four 2 μs; eight 1 μs; sixteen 0.5 μs and eighty 0.1 μs. Moreover, the 8 μs trajectory was further extended to 16 μs to have reference values of the diverse properties measured. As a conclusion our results suggest that a few short MD trajectories might provide a better sampling than one unique trajectory. However, caution should be exercised since short trajectories need to be long enough to overcome local barriers surrounding the starting point. An effective way to get insight into the minimum MD trajectory length requires monitoring the convergence of a structural feature, as for example the helical content of the peptide.

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