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Force field comparison: Amber, GROMOS, CHARMM, OPLS
Force field comparison: Amber, GROMOS, CHARMM, OPLS:
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
What is in the movie:
The movie spans 0-10 and 990-1000ns of the 1000ns trajectory. For clarity, water, ions and hydrogens are not shown and rotation and translation of the peptide has been removed.
Secondary structures (mostly visible in the 990-1000ns part) were colored as follows:
– yellow – β-sheet (arrows indicate chain direction)
– purple – alpha helix
– blue – 310 helix
– white – coil