STEP

NAME
STEP - Set up input information on the frequency of the ensemble transitions and on the free energy updating options.

SYNOPSIS
STEP $L_c$ $L_a$ $L_b$ $[n_{av}]$

DESCRIPTION
This command defines the following parameters. $L_c$ (real number): time interval (in fs) used to attempt a transition of a replica between adjacent ensembles [see point (4) in Section 6.3.2]; $L_a$ (real number): time interval (in fs) used to store the dimensionless works $W[n \rightarrow n+1]$ and $W[n \rightarrow n-1]$ [see point (2) in Section 6.3.2]; $L_b$ (real number): time interval (in fs) used to try a free energy update [see point (3) in Section 6.3.2]; $n_{av}$ (integer number): number of independent free energy estimates used to update the weighted free energy averages [see Section 6.3.3]. The parameter $n_{av}$ is optional. If $n_{av} = 0$ or not reported in the input, then all free energy estimates stored during the run are used.
IMPORTANT NOTE: it is also possible to change $n_{av}$ ``on-the-fly'' during the simulation. In such a case a file called SGE_DF_FLY.set must be created by the user in the working directory (when using the serial version of ORAC ) or in the parent directory of PARXXXX directories (when using the parallel version of ORAC ). Such a file must contain an integer number alone, which corresponds to $n_{av}$ (additional characters will be ignored). Note also that if this option is employed then an additional working file, called SGE_DF_FLY.dat, will be created by the program in the same directory. This file contains information related to the single estimates of free energy differences (do not remove it when restarting from a previous run). If the file SGE_DF_FLY.set is removed after a simulation and a new simulation is restarted, then this latter simulation continues as if the former simulation had been launched with the STEP command specified in the input file.

EXAMPLES
STEP 5. 10. 2000. 40
Ensemble transitions are attempted every 5 fs; dimensionless works are stored every 10 fs; free energy updates are attempted every 2000 fs; the last 40 free energy estimates are used in the weighted free energy average of Eq. 6.28.

DEFAULTS
The only allowed default value is related to $n_{av}$ ( $n_{av} = 0$). In such a case, all free energy estimates are used in the weighted free energy average.

WARNINGS
If STEP is not set in the input, then default values are employed. Default values are $L_c = tstep$, $L_a = tstep$, $L_b = 1000 \times tstep$ and $n_{av} = 0$, where $tstep$ is the simulation time step (in fs) of the $h$th intermolecular shell (see Section 4.3).