Chemistry Reference
In-Depth Information
to extend those time scales by using different simplifying assumptions and
approximations including, for example, two-state transitions, equilibrium dis-
tributions along the path, or, removal of high-frequency motions. Therefore,
path methodologies can extend the range of application of computer simulation,
but they do so with loss of accuracy and dynamical information when compared
with normal and MTS molecular dynamics simulations. Some path techniques
utilize MD to compute rate constants and to recover part of the dynamical prop-
erties that have been filtered out. Use of MTS should improve the efficiency and
practicality of these calculations in the future.
APPENDIX: MATLAB SCRIPTS FOR THE MTS
TUTORIAL
function [t,x,v,eout]
¼
dyntwowaters(h,nstep,x0,v0,
tau,method)
%[t,x,v,eout]
¼
dyntwowaters(h,nstep,x0,v0,tau,
method)
% Dynamics front-end for model system introduced in
Cardenas & Barth 2007
%INPUT ARGUMENTS, with some values used in Cardenas
&Barth
% h timestep, h
¼
0.01
% nstep number of integration steps
% x0 init. postions, x0
¼
[0 0 0.95 0 0 0.95 5
1.0 4.05
15
0.05]'
% v0 vector of initial atom velocities, v0
¼
zeros
(12,1)
% tau number of steps between slow force evaluations
% method string specifies integration method, 'v',
'i', 'b', 'e'
%OUTPUT ARGUMENTS
% t vector of time values
% x trajectory of positions
% v trajectory of velocities
% eout energy along computed trajectory
%
%Eric Barth
%Kalamazoo College, 2007
