Evidence map›Paper›PMID 31575198›Full record

ArticleThe Journal of chemical physics2019

Mapping saddles and minima on free energy surfaces using multiple climbing strings.

Gourav Shrivastav, Eric Vanden-Eijnden, Cameron F Abrams

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Gourav ShrivastavDepartment of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA.ORCID 0000000259067272
Eric Vanden-EijndenCourant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA.
Cameron F AbramsDepartment of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA.ORCID 0000000212400816

Funding

Transition Path Theory and Markovian Milestoning for Prediction of Protein-Ligand Binding Kinetics in Molecular SimulationsR01GM100472 · NIGMS · DREXEL UNIVERSITY · PI ABRAMS, CAMERON F · 2011 to 2020
$2.5M
NIGMS NIH HHS R01 GM100472
6 · The paper itself

Abstract

Locating saddle points on free energy surfaces is key in characterizing multistate transition events in complicated molecular-scale systems. Because these saddle points represent transition states, determining minimum free energy pathways to these saddles and measuring their free energies relative to their connected minima are further necessary, for instance, to estimate transition rates. In this work, we propose a new multistring version of the climbing string method in collective variables to locate all saddles and corresponding pathways on free energy surfaces. The method uses dynamic strings to locate saddles and static strings to keep a history of prior strings converged to saddles. Interaction of the dynamic strings with the static strings is used to avoid the convergence to already-identified saddles. Additionally, because the strings approximate curves in collective-variable space, and we can measure free energy along each curve, identification of any saddle's two connected minima is guaranteed. We demonstrate this method to map the network of stationary points in the 2D and 4D free energy surfaces of alanine dipeptide and alanine tripeptide, respectively.

Identifiers

PMID31575198
PMCPMC7043847

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.