Environments, Commands and Sub-commands

The following 10 environments are available:

1

&ANALYSIS retrieves the history file.

2

&INOUT contains commands concerning input/output operations which can be carried out during run time. The commands allowed within the INOUT environment write history files in different formats and dump the restart files.

3

&INTEGRATION includes commands defining the integration algorithms to be used during the simulation run.

4

&META includes commands defining the metadynamics simulation.

5

&POTENTIAL includes commands which define the general features of the system interacting potentials. These features are common to both solute and solvent and concern only the non-bonded interactions.

6

&PROPERTIES includes commands which make ORAC  compute run time observables. The commands allowed within the &PROPERTIES environment can compute on the fly: pair correlation functions, static structure factors and velocity auto-correlation function. This environment is not supported.

7

&REM setup the Replica Exchange simulation (work only with the parallel version).

8

&RUN defines run time parameters which concern output printing and run averages.

9

&SETUP includes commands concerned with the simulation box setup. In this environment, the simulation cell parameters, dimensions and symmetry can be initialized. Moreover, files containing the system coordinates in appropriate format can be provided.

10

&SIMULATION includes commands which define the type of simulation that is to be carried out. In particular, commands are available to run steepest descent energy minimization, and molecular dynamics simulations in various ensembles.

11

&SOLUTE includes commands which are concerned with specific aspects of the solute force field and structure.

12

&SOLVENT includes commands which are concerned with specific aspects of the solvent force field and structure.

13

&ST setup the Serial Generalized Ensemble simulation (work with both serial and parallel versions).

14

&PARAMETERS includes commands which read the topology and force field parameter files of the solute. These files contain sufficient information to define the solute topology and to assign potential parameters to the solute molecules.