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. Author manuscript; available in PMC: 2011 Jun 15.
Published in final edited form as: J Phys Chem B. 2009 Jul 2;113(26):9004–9015. doi: 10.1021/jp901540t

Figure 5.

Figure 5

Temperature dependence of helix formation in Ac-(AAQAA)3-NH2. (A) Fraction helix as a function of temperature for ff03 (blue squares) ff99SB (red triangles), and the revised force fields ff03* and ff99SB*; experimental estimate from NMR chemical shifts given as magenta circles. (B) Effects of simulation parameters on results: ff03 (blue squares), ff03 run with Amber 10 instead of Gromacs 3.3.1 (blue circles), ff03 with TIP4P-Ew instead of TIP3P (blue triangles), ff03* (black filled squares), ff03* starting from helical conformations in all replicas (black open circles), ff03* with simulation cell with 6.1% larger volume (black triangle up), ff03* with simulation cell with 5.9 % smaller volume (black triangle down), ff03* with 45 Å simulation cell (black open squares), ff99SB (red triangle up), ff99SB from helix (red circles); experimental data as in (A). The convergence of the calculated helical fraction is shown by plotting a cumulative fraction helix against time for simulations with ff03* at temperatures of (C) 303 K, (D) 355 K and (E) 396 K. Symbols in (C)–(E) as in (B). Where error bars are not visible, they are smaller than the symbol size.