Force field comparison: Snapshot 2: Amber, GROMOS, CHARMM, OPLS

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.

 

Proteins explain very briefly:

 

- This is a link to a very brief intro to proteins disordered and regular. Note, the presentation at this link has lots of links to outside resources, just hover your mouse around the pics and terms to see the links.

 

 

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

 

 

Who:

 

This study was a collaboration between the SoftSimu Group and Choy Lab

 

 

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).

 

3. Accelerating the Conformational Sampling of Intrinsically Disordered Proteins, Trang Nhu Do, Wing-Yiu Choy, and Mikko Karttunen, J. Chem. Theory and Comput. 10, 5081–5094 (2014).

 

4. Conformational biases of linear motifs, Elio A. Cino, Wing-Yiu Choy, Mikko Karttunen, J. Phys. Chem. B 117, 15943–15957 (2013).

 

 

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)

Done