To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal peptide from p53 confirming its performance nearly equal to the original REST.
We address the metric reconstruction problem of such filamentary
Structures from data sampled around them. We prove that they can be
Approximated, with respect to the Gromov-Hausdorff distance by well-chosen Reeb
Graphs (and some of their variants) and we provide an efficient and easy to
An easy-fitting and trustworthy scoring system can be directly developed using a naïve Bayes approach. The simplicity of its design allows the system to be customized to any specific institution and updated regularly. This aspect has important practical implications because it can encourage the use...
MDMP is a new parallel programming approach that aims to provide users with
an easy way to add parallelism to programs, optimise the message passing costs
of traditional scientific simulation algorithms, and enable existing MPI-based
parallel programs to be optimised and extended without requiring...
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