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Preface
This manual is for version 5.0 of the program ORAC .1
In this
new release many improvements have been included. Here, we only
mention the most important new features.
- Now ORAC may be run in parallel using the standard message passing
interface libraries (OpenMPI, mpich2). The parallelism allows to run
(Hamiltonian) replica exchange simulations and multiple walkers
metadynamics simulations. The REM algorithm may be implemented
in a ``solute tempering'' fashion allowing potential scaling only for
limited (user selected) part of the simulated system,.
- ORAC can run steered molecular dynamics non equilibrium
trajectories with on the fly work evaluation. The driven coordinate
can be any combination of intramolecular coordinates (stretching
bending and torsions). This features allows one to compute along
the selected ``reaction coordinate'' the free energy profile (PMF)
using non-equilibrium Jarzinsky and Crooks theorem . Steered
molecular dynamics can be done as well by varying the temperature of the
Nosé bath doing on the system an adimensional work computed
according to the generalized Crooks theorem.
- Minimization routines has been improved by providing the
possibility of minimizing only part of the solute by keeping
frozen all other degrees of freedom.
- several ancillary programs are included in this distribution
for post analysis of steered molecular dynamics and
replica exchange simulation data.
The present manual is organized as follows: The first seven chapters
constitute the ORAC theoretical background. Chapter 1) contains
general and introductory remarks. Chapter 2) deals with symplectic
and reversible integrators and introduces to the Liouvillean
formalism, Chapter 3) extends the Liouvillean formalism to the
extended Lagrangian methods and Chapter 4) describes how to deal with
long range electrostatic interactions and how to combine the SPME
method with the multilevel integration of the equations of motion in
order to obtain efficient simulation algorithms. Chapter for 5 to 7
have been added in the present release. Chapter 5) contains an
introduction to replica exchange techniques and a description on how
such a technique has been implemented in the ORAC program. Chapter
6) deals with metadynamics simulations. Chapter 7) treats steered
molecular dynamics simulation and the theory of non equilibrium
processes. Chapter 8) is the command reference of the ORAC program. Chapter
9) contains instructions on how to compile and run ORAC in a serial and
parallel
environment.
Next: Atomistic simulations: an introduction
Up: orac-manual
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