## This is an example data file for jfm2full.c
##
## The following line specifies the total number of the model segments.
Number of segments                 38

## The next line defines the length of each segment in base pairs.
## All segments have the same length. This line is necessary
## for conversion of the result to moles per liter.
Segment length                     5.25

## The next line specifies the segment diameter-to-length ratio.
## Any non-zero value turns on hardcore excluded-volume interactions 
## and makes the chain self-avoiding. Use this feature only 
## if you are absolutely sure that these effects are important 
## because the program will run considerably slower. 
Diameter-to-length ratio           0.0

## The next part contains detailed description of all the model
## chain segments. Each line contains 6 numbers:
## *   number of sequential segments of a certain kind.
## *   then THREE Euler angles in radians describing
## *   the equilibrium bend and twist in each segment of the kind.
## *   then rms fluctuations of the twist, rmst. This is 0.175
## *   for 5.25-bp segments if torsional rigidity is 2.4e-19 erg*cm.
## Then rms fluctuations of the bend, rmsb. More precisely rmsb
## *   is the specified below. It equals to 0.193
## *   for 5.25-bp segments if the persistence length is 48.5 nm.
## The values of rmst and rmsb are connected with the length of one
## *   segment, L, and the bending and torsional rigidities of a
## *   segment, g and C:
##
##               rmst=sqrt(L*kT/C),   rmsb=sqrt(L*kT/g),
##
## *   where kT is the Boltzmann temperature factor. The value of g 
## *   is directly related with the persistence length of a polymer 
## *   chain, a:
##                              a=g/kT.
##
## The following set of segments corresponds to
##    13 straight segments; for simplicity twist of all segments equals 0;
##     1 intrinsically bend segment, beta=0.262;
##     1 straight segment, beta=0.262;
##     1 intrinsically bend segment, beta=0.262;
##    17 straight segments;
##     1 straight segments represents the single-stranded linker;
##     4 straight segments;
Segments: number alpha beta gamma dac db
 13    0.0  0.0     0.0   0.175  0.193
  1    0.0  0.262   0.0   0.175  0.193
  1    0.0  0.0     0.0   0.175  0.193
  1    0.0  0.262   0.0   0.175  0.193
 17    0.0  0.0     0.0   0.175  0.193
  1    0.0  0.0     0.0   5.60   0.635
  4    0.0  0.0     0.0   0.175  0.193

## The next line specifies the desired linking number of the model
## chain in the circular topoisomer.
Linking number                     0

## The next part is the restrictions on twist and bend
## angles and distance between the chain ends that provide
## an accurate calculation of the j-factor in most cases.
## They can also be used to remove certain restrictions altogether.
## First two numbers are in radians. The last is in base pairs.
Conformation restriction: tw bd r
0.1 0.1 3.1

## The next is the number of Metropolis movements for evaluation
## of each conditional probability. Increase it to improve the accuracy.
Number of movements                100000