Force field comparison: Snapshot 2: Amber, GROMOS, CHARMM, OPLS by softsimu on Flickr.A través de Flickr: Snapshots from a comparison of secondary structure formation using different force fields in microsecond molecular dynamics simulations. All simulations were started from the same initial conditions. We tested the following force fields: Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27 and OPLS-AA/LSnapshots: The snapshots show the final configurations after one microsecond. The secondary structures are clearly different. An illustration of the compexity of the potential landscape is shown. Interaction between D77 and T80 typically precedes hairpin formation. This interaction is formed in the first 10ns in the Amberff99SB*-ILDN trajectory. FULL MOVIES: SInce flickr limits movies to 90 secs, the section 990-1000 ns is not visible here. For the full movie, please see: Full movie at YouTubeSee also: 1. Force field comparison: Snapshot 1: Amber, GROMOS, CHARMM, OPLS 2. Force field comparison: Single peptide using Amber99SB* 3. Microsecond atomistic MD simulation: Transition of the 9-mer mouse Neh2 peptide from an extended to beta-turn conformation. 4. Convergence of the 32-mer mouse Neh2 peptide to a bound-state-like β-turn conformationComputational resources: - SharcNetReferences: 1. Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations, Elio A. Cino, Wing-Yiu Choy and Mikko Karttunen, J. Chem. Theory and Comput. 8, 2725–2740 (2012). 2. Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response, Elio Cino, Jirasak Wong-ekkabut, Mikko Karttunen, Wing-Yiu Choy,PLoS One 6, e27371 (2011).See also: - Assessment of common simulation protocols for simulations of nanopores, membrane proteins & channels, J. Wong-ekkabut & M. Karttunen, J. Chem. Theory and Comput. 8, 2905–2911 (2012)
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Force field comparison: Snapshot 2: Amber, GROMOS, CHARMM, OPLS by softsimu on Flickr.

A través de Flickr:
Snapshots from a comparison of secondary structure formation using different force fields in microsecond molecular dynamics simulations. All simulations were started from the same initial conditions.

We tested the following force fields: Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27 and OPLS-AA/L

Snapshots:

The snapshots show the final configurations after one microsecond. The secondary structures are clearly different. An illustration of the compexity of the potential landscape is shown.


Interaction between D77 and T80 typically precedes hairpin formation. This interaction is formed in the first 10ns in the Amberff99SB*-ILDN trajectory.

FULL MOVIES: SInce flickr limits movies to 90 secs, the section 990-1000 ns is not visible here. For the full movie, please see: Full movie at YouTube

See also:

1. Force field comparison: Snapshot 1: Amber, GROMOS, CHARMM, OPLS

2. Force field comparison: Single peptide using Amber99SB*

3. Microsecond atomistic MD simulation: Transition of the 9-mer mouse Neh2 peptide from an extended to beta-turn conformation.

4. Convergence of the 32-mer mouse Neh2 peptide to a bound-state-like β-turn conformation



Computational resources:

- SharcNet



References:

1. Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations, Elio A. Cino, Wing-Yiu Choy and Mikko Karttunen, J. Chem. Theory and Comput. 8, 2725–2740 (2012).

2. Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response, Elio Cino, Jirasak Wong-ekkabut, Mikko Karttunen, Wing-Yiu Choy,PLoS One 6, e27371 (2011).

See also:

- Assessment of common simulation protocols for simulations of nanopores, membrane proteins & channels, J. Wong-ekkabut & M. Karttunen, J. Chem. Theory and Comput. 8, 2905–2911 (2012)

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