SETUP

 NAME
SETUP – Define the scaling in a REM simulation.

 SYNOPSIS
SETUP $scale_1$ [$scale_2$ $scale_3$] irest

 DESCRIPTION
The SETUP command is used to define the lowest scaling factor(s) (i.e the highest temperature) of the last replica. The number of replicas in the REMD simulations are equal to the number of processors passed to the MPI routines (nprocs). The spacing between the replicas can be defined in the REM.set user-file by setting the irest integer equal to 2. If only the $scale_1$ real parameter is specified, an equal scaling is applied to all parts of the potential. If the three parameters $scale_1$, $scale_2$, $scale_3$ are specified, then $scale_1$ refers to the bending, stretching and improper torsional potential, $scale_2$ to the (proper) torsional potential and to the 14 non-bonded interactions and finally $scale_3$ refers to the non bonded potential.NB: when the Ewald summation is used together with the command SEGMENT(&REM), $scale_3$ scales only the direct (short-ranged) part of the electrostatic interactions and the (long-ranged) reciprocal part has a scaling factor of 1.0 (i.e. these interaction are not scaled). If irest=0, the run is restarted from a previous one. This implies that the directories PARXXXX are present and are equal in number to nprocs as specified in the mpiexec/mpirun command. The default prefix of the REM directories can be changed from PAR to anything by specifying in the preamble of the main input file the shebang directive

#!&MYPREFIX

If irest$\ne 0$ then the run refers to a cold start from scratch and

• if irest$=1$, then the scaling factors of the intermediate replicas are derived according to a geometric progression, namely $scale_i(m) = scale_i^{m/(nprocs -1)}$, where $scale_i(m)$ is the scaling factor for the potential $i$ of the replica $m$ with $0\le m \le nprocs-1$. For example, if $scale_i = 0.6$ and nprocs=4, then replica $m=0$ has $scale_i(0)=1$, replica $m=1$ has $scale_i(1) = 0.843433$, replica $m=2$ has $scale_i(2) = 0.711379$ and the replica $m=3$ has $scale_i(3) = scale_i = 0.6$.
• if irest$=2$, the scaling factors are read from an auxiliary file called “REM.set” that must be present in the directory from which the program is launched using the mpiexec/mpirun command. This ASCII file has as many lines as parallel processes and on each line the three (or one) scale factors must be specified.
• if irest$=3$, then each replica read from a user-defined pdb file that must reside in the PARxxx dir. This is useful when restarting a REM simulation with the SAVE_ALL_FILES directive. To restart a REM with the SAVE_ALL_FILES directive on, the user must hence do the following: 1) set irest to 3 in the main rem input; 2) change the filename specification in the SAVE_ALL_FILES directive (namelist &INOUT) ; this avoids overwriting the saved restart files ; 3) copy the last configuration in the PARxxx pdb files to a common user-name file in the same directories (e.g. RESTART.pdb) and instructs the program to read from that PDB in the namelist &SETUP using the directive READ_PDBb RESTART.pdb with no ../ specification ;4) optionally rename in the main input the output files to be produced during the rem simulation.

 EXAMPLES
SETUP 1.0 1.0 0.6 1
Scales only the non bonded potential (direct part) using a geometric progression.

 DEFAULTS
SETUP 1.0 1.0 1.0 1