Methanol

A system of 216 all atom Methanol molecules (1296 interaction sites) with a density of .8300 g/cm**3 is read from a mos.structure-file. Velocities are also obtained from the file.

The particle mesh Ewald (PME) algorithm is employed by using a 20x20x20 grid and b-spline interpolation of 4'th order (Momentum conservation is forced). The real space sum energies and forces are linearly interpolated from lookup tables.

The nonbonded interactions and real space terms are truncated at a cutoff of 9.0 A. The Verlet-neighborlist cutoff is set to 11.0 A. Neighborlist updating is done automatically due to particle displacement.

The system is simulated for 100 steps at 300 K and 1 atm with a timestep of 1.0 fs. Weak coupling is used to control temperature and pressure : Coupling-constant of 2.0 ps**(-1) and 5.0 10**(-4) MPa**(-1)ps**(-1) are employed for temperature and pressure, respectively.

Distance constraints are solved by using the SHAKE algorithm. A tolerance of 10**-4 is allowed.

The system-file can be easily generated by using the mmf-file and the AMBER forcefield employing the ffparse command.

ffparse -ff ../../forcefield/lib/AMBER_parm94.ff -mmf meoh.mmf -fix