1549380323-Statistical Mechanics Theory and Molecular Simulation

Examples 129

Fig. 3.8 (Top) Ball-and-stick model of the isolated alanine dipeptide. (Bottom) Schematic
representation of the alanine dipeptide, showing the anglesφandψ.

Problem 3.3). The three constraints in each molecule are treated with the explicit
matrix version of the constraint algorithms described in Section 3.9.
In this simulation, the dipeptide is solvated in a cubic box of length 25.64 ̊A on a
side containing 558 water molecules for a total of 1696 atoms. A simulation of 1.5 ns

0 400 800 1200

t (ps)

0

1 ́ 10 -5

2 ́ 10

-5

3 ́ 10 -5

4 ́ 10

-5

5 ́ 10 -5

DE

0 400 800 1200

t (ps)

280

290

300

310

320

T

(K)

Fig. 3.9(Left) Instantaneous and cumulative energy conservation measures for the alanine
dipeptide in water. (Right) Instantaneous and cumulative temperature.

is run using the RESPA integrator of Section 3.11 with a small time stepof 1.0 fs and
a large time step of 6.0 fs. The reference system includes all intramolecular bonding
and bending forces of the solute. Fig. 3.9 shows energy conservation of eqn. (3.14.1)
and its instantaneous fluctuations as well as the cumulative average and instantaneous
temperature fluctuations produced by the total kinetic energy divided by (3/2)Nk. It