ArticleJournal of molecular modeling2026
Error estimation on the box size correction formula of diffusion coefficient in molecular simulations.
Article in Journal of molecular modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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.
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.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
contextCorrecting the diffusion coefficient for simulation box size is an essential step in extrapolating small simulations to real systems. The current common approach is a correction formula based on fluid dynamics theory, introduced by Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)]. While this formula has been used by some authors for theoretical correction, others have found some difficulties in applying the formula. In this paper, we have reviewed the error issues in diffusion coefficient calculations in molecular simulations and discussed why significant uncertainties arise when applying the Yeh-Hummer correction formula. Furthermore, based on mathematical statistics theory, we suggest using a new correction formula that converges more quickly to the particle number, aiming to achieve better correction results. Using molecular dynamics simulation data of Lennard-Jones fluids, the dependence of the diffusion coefficient on different powers of the number of particles is investigated. It shows that our formula is slightly better than Yeh-Hummer's formula in agreement with the simulation results.
methodMolecular dynamics simulations were carried out in the NVT ensemble using parallel simulator-LAMMPS. The simulations were run in the reduced unit. The interaction potential was chosen to be Lennard-Jones 12-6 model. The Nose-Hoover thermostat was used to realize a thermal equilibrium state. A cutoff distance was taken as 2.5 times the Lennard-Jones interaction diameter. The time steps were all taken as 0.005 in reduced units. A typical total number of simulation steps was 3.5 × 10
Indexed as
Identifiers
42149264What OpenQuestion holds
Registered trials
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.