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. Author manuscript; available in PMC: 2012 Jun 16.
Published in final edited form as: J Phys Chem A. 2011 Apr 18;115(23):6137–6148. doi: 10.1021/jp111093c

Figure 4.

Figure 4

A periodic box of water that was used in the simulation of a conformational transition in adenosine. The molecule is solvated with 420 TIP3P water molecules 49 with a periodic cubic box of 23.8×23.8×23.8Å3. The box size is adjusted to give a pressure of ~1atm at 300K. We used a matrix variant50 of the SHAKE algorithm 51 to fix water bond lengths and angles while the solute is not constrained. 8Å cutoff is used for Lennard Jones and 8.5 Å for real space cutoff of electrostatics. Particle-mesh Ewald summation was used for long range electrostatics. The time step was 2fs. All simulations are performed with AMBER/OPLSAA force field where bonding terms are taken from Amber99 52 and the nonbonding terms are from OPLSAA 53. The parameters are available from MOIL 54 http://clsb.ices.utexas.edu/prebuilt/