Evidence map›Paper›PMID 25400877›Full record

ArticleThe journal of physical chemistry letters2014

Building Water Models: A Different Approach.

Saeed Izadi, Ramu Anandakrishnan, Alexey V Onufriev

Abstract read
In one paragraph

Article in The journal of physical chemistry letters, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 668 papers.

0numbers the graph read from it
0cells of the map it votes in
668citing 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

668 citing papers in PubMed.

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608 more citing papers are in PubMed but not listed here.

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.

Saeed IzadiDepartment of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer Science and Physics, Virginia Tech , Blacksburg, Virginia 24060, United States.
Ramu AnandakrishnanDepartment of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer Science and Physics, Virginia Tech , Blacksburg, Virginia 24060, United States.
Alexey V OnufrievDepartment of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer Science and Physics, Virginia Tech , Blacksburg, Virginia 24060, United States.

Funding

Analytical Electrostatics: Methods and Biological Applications.R01GM076121 · NIGMS · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI ONUFRIEV, ALEXEY VLAD · 2006 to 2014
$2.6M
NIGMS NIH HHS R01 GM076121
6 · The paper itself

Abstract

Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than the symmetry. Instead, we optimize the distribution of point charges to best describe the "electrostatics" of the water molecule. The resulting "optimal" 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures. The improvements in the proposed model extend beyond bulk properties: compared to common rigid models, predicted hydration free energies of small molecules using OPC are uniformly closer to experiment, with root-mean-square error <1 kcal/mol.

Identifiers

PMID25400877
PMCPMC4226301

What OpenQuestion holds

Textmetadata
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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.