VOLUME 291 (2016) PAGES 22093–22105

In the “Materials and Methods” section, the conversion of the reduced time unit to a real time unit (Δ

*t** = 0.072 ns) was incorrect. The correct value should be Δ*t** = 0.96 ns. Thus, the longest time accessed in the single DMD simulation should have been 672 μs, which corresponds to 2000 billion collisions. The simulation times (*x*axes) in Figs. 1, 6, 7, and 9 and Figs. S1–S5 and Table 2 as well as in other places in the context of the article should all be multiplied by a factor of 29. The correct calculation procedures are described below.The way that we relate the reduced time unit to the real time unit is to compare the self-diffusion coefficient of Aβ(16–22) peptide obtained from DMD simulation (

*D*_{DMD}) and atomistic molecular dynamics (MD) simulation (*D*_{MD}) at*T*= 298 K. The reduced temperature of the self-diffusion coefficient measurement in DMD simulation is chosen to be*T** = 0.181, which corresponds to room temperature (*T*= 298 K) according to temperature scaling (Wang, Y., Shao, Q., and Hall, C. K. (2016) N-terminal prion protein peptides (PrP(120–144)) form parallel in-register β-sheets via multiple nucleation-dependent pathways.*J. Biol. Chem.***291,**22093–22105),*T** = (*T*+ 115.79)/2288.46 = (298 + 115.79)/2288.46 = 0.181.The self-diffusion coefficients in both DMD and MD simulation are calculated using the Einstein equation. We plotted the mean square displacement (MSD) of N Aβ(16–22) peptides

where Δ

*versus*time for both atomistic MD simulation (*N*= 1) and DMD simulation (*N*= 6), as shown in Fig. 11,*A*and*B*, by using the following equation,$\text{MSD}\left(t+\Delta t\right)=\text{MSD}\left(t\right)+\overline{{d}^{2}}=\text{MSD}\left(t\right)+\frac{{\displaystyle {\sum}_{i=1}^{i=N}{\left|{r}_{i}^{t+\Delta t}-{r}_{i}^{t}\right|}^{2}}}{N}$

(Eq. 1)

where Δ

*t*is the time unit;*N*is the total number of peptides;*d*^{2}is the averaged square displacement of*N*peptides; and*r*_{i}^{t+Δt}and*r*_{i}^{t}are the coordinates of the*i*th peptide at*t*+ Δ*t*and*t*. For DMD simulation,*t** is used in DMD instead of*t*to represent reduced time.Using the MSD data in Fig. 11,

*A*and*B*, we obtain the self-diffusion coefficients*D*_{MD}and*D*_{DMD}.${D}_{\text{MD}}=\frac{1}{6}\frac{\text{MSD}\left({t}_{2}\right)-\text{MSD}\left({t}_{1}\right)}{{t}_{2}-{t}_{1}}=\frac{48.11-27.45}{6\times \left(17.80-10.66\right)}=0.48{\text{nm}}^{2}/\text{ns}$

(Eq. 2)

${D}_{\text{DMD}}=\frac{1}{6}\frac{\text{MSD}\left(t{*}_{2}\right)-\text{MSD}\left(t{*}_{1}\right)}{t{*}_{2}-t{*}_{1}}=\frac{328.57-109.01}{6\times \left(120.01-40.01\right)}=0.46{\text{nm}}^{2}/\Delta t*$

(Eq. 3)

By equating the self-diffusion coefficients calculated from both atomistic MD simulation and DMD simulation, we obtain the reduced time unit in DMD simulation in terms of the real time unit to be 1 (Δ

*t**) = 0.96 ns.## Article info

### Publication history

Published online: December 15, 2017

### Identification

### Copyright

© 2017 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.

### User license

Creative Commons Attribution (CC BY 4.0) | How you can reuse

Elsevier's open access license policy

Creative Commons Attribution (CC BY 4.0)

## Permitted

- Read, print & download
- Redistribute or republish the final article
- Text & data mine
- Translate the article
- Reuse portions or extracts from the article in other works
- Sell or re-use for commercial purposes

Elsevier's open access license policy