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 bewteen the replicas is controlled
by the irest integer. If only the scale1 real parameter is specified,
an equal scaling is applied to all parts of the potential. If
the three parameters scale1, scale2, scale3 are specified,
then scale1 refers to the bending, stretching and improper
torsional potential,
scale2 to the (proper) torsional potential and to the 14
non-bonded interactions and finally scale3 refers to the non
bonded potential.NB: when the Ewald summation is used scale3
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
i) the directories PARXXXX are present and are equal in number to
nprocs as specified in the mpiexec/mpirun command and that ii) each
of these nprocs directories
contains the PARA_RESTART file bearing the current replica index
and the corresponding scaling factors.
If irest
then
the run refers to a cold start from scratch and
- if irest
, then the scaling factors of the intermediate
replicas are derived according to a geometric progression, namely
scalei_m=scalei
, where scalei_m is the
scaling factor for the potential
of the replica
with
.
For example, if scalei
and nprocs=4, then
replica
has scalei_0=1, replica
has
scalei_2= 0.843433 ,replica
has
scalei_2= 0.711379 and the replica
scale_3=scalei=0.6.
- if irest
, 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.