2023
DOI: 10.1021/acs.jcim.3c01072
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Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation

Diship Srivastava,
Niladri Patra

Abstract: Previously, it was shown that the telescoping box scheme, in combination with adaptive steered molecule dynamics (ASMD), can be used to estimate the potential of mean force (PMF) with a decrease in computational cost associated with large solvation boxes. Since ASMD reduces to umbrella sampling (US) in the limit of infinitely slow pulling velocity, a hypothesis was made that the telescoping box scheme can be extended to include the US method. The hypothesis was tested using the unfolding pathway of a polyalani… Show more

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Cited by 2 publications
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“…A total of 6 ns simulation was performed in each window followed by short energy minimization and equilibration to avoid the unnecessary overlapping of the atom coordinates. The WHAM calculation was performed for each umbrella window along the RC, and the Monte Carlo bootstrap , was performed to estimate the statistical uncertainty of the PMF profile, and the tolerance for iteration was set to be 0.000001 to obtain a convergent free energy plot. To keep the simulation consistent with the prior one, the temperature was set to be 300 K, a commonly used temperature for modeling biomolecular systems.…”
Section: Methodsmentioning
confidence: 99%
“…A total of 6 ns simulation was performed in each window followed by short energy minimization and equilibration to avoid the unnecessary overlapping of the atom coordinates. The WHAM calculation was performed for each umbrella window along the RC, and the Monte Carlo bootstrap , was performed to estimate the statistical uncertainty of the PMF profile, and the tolerance for iteration was set to be 0.000001 to obtain a convergent free energy plot. To keep the simulation consistent with the prior one, the temperature was set to be 300 K, a commonly used temperature for modeling biomolecular systems.…”
Section: Methodsmentioning
confidence: 99%