A replica exchange Monte Carlo algorithm for protein folding in the HP model (REMC-HPPFP)
===============================================================
PARAMETERS:

The following parameters need to be specified:

parameter            description
--------------------------------
-seq                 hp sequence to be folded in lower case letters (e.g. hhhhpppphhh)
-eng                 optimal energy (specify as a positive value) known or approximated (if not known use large enough number) 
-tracFile            output file
-minT                minimum temperature of any replica
-maxT                maximum temperature of any replica
-numReps             number of replicas
-numLocalSteps       number of local steps to perform in each subsidiary Monte Carlo search, prior to replica exchange
-expID		     experiment ID: used to output some trace information
-maxRuntime	     maximum runtime in CPU seconds

Optional:

parameter            description
--------------------------------
-seed                a seed for random number generation can be supplied in order to reproduce results
-pmWeight	     when using the 'mixed moveset', the weight to give pullmoves vs. local moves

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EXAMPLES OF USAGE:

folding in 2D (pullmoves):

./rem2dpm -minT 160 -maxT 220 -numReps 5 -numLocalSteps 500 -seed 1523772276 -seq hhhhhhhhhhhhphphpphhpphhpphpphhpphhpphpphhpphhpphphphhhhhhhhhhhh -eng 42 -maxRunTime 3600 -expID eS1-8-pullmoves_1 -traceFile eS1-8-pullmoves_1.sqt

folding in 3D (mixed moveset):

./rem3dm -minT 160 -maxT 220 -numReps 2 -numLocalSteps 500 -pmWeight 0.5 -seed 1584092599 -runs 1 -seq phhphhhphhhhpphhhpppppphphhpphhphppphhphphphhppp -eng 31 -maxRunTime 3600 -expID eS2-8-mixed_1 -traceFile eS2-8-mixed_1.sqt

==================================================================
OUTPUT:

Console output produced (2D pullmoves example):

REMC-HP2D-PM

Begin Simulation
0.01: Current Best Solution: -13
0.01: Current Best Solution: -17
0.02: Current Best Solution: -19
0.03: Current Best Solution: -21
0.04: Current Best Solution: -24
0.05: Current Best Solution: -26
0.05: Current Best Solution: -27
0.1: Current Best Solution: -29
0.12: Current Best Solution: -30
0.14: Current Best Solution: -31
0.14: Current Best Solution: -32
0.18: Current Best Solution: -35
1.04: Current Best Solution: -36
1.18: Current Best Solution: -37
1.49: Current Best Solution: -38
1.5: Current Best Solution: -39
1.51: Current Best Solution: -40
1.89: Current Best Solution: -41
8.53: Current Best Solution: -42
Real time: 8.53

ggslsrrsllrsrrlrlrrllrrllrrlrrllrrllrrlrrllrrllrrlrlrrsrlssslsll


                        
   p--p  p--p  p--p   
   |  |  |  |  |  |     
p--h  h--h  h--h  h--p
|                    |  
p--h  H  h--h--h  h--p
   |  |  |     |  |     
p--h  h  h--H  h  h--p
|     |        |     |  
p--h  h--h--h  h  h--p
   |        |  |  |     
p--h  h--h--h  h  h--p
|     |        |     |  
p--h  h--h  h--h  h--p
   |     |  |     |     
   p--h  h  h  h--p   
      |  |  |  |        
      p--h  h--p      

End Simulation


Console output produced (3D mixed example):


REMC-HP3D-M

Begin Simulation
5.88722e-17: Current Best Solution: -11
1.03026e-16: Current Best Solution: -14
1.4718e-16: Current Best Solution: -18
0.01: Current Best Solution: -19
0.01: Current Best Solution: -20
0.01: Current Best Solution: -21
0.01: Current Best Solution: -22
0.02: Current Best Solution: -23
0.02: Current Best Solution: -26
0.03: Current Best Solution: -27
0.08: Current Best Solution: -28
0.15: Current Best Solution: -29
0.38: Current Best Solution: -30
0.39: Current Best Solution: -31
Real time: 0.39
End Simulation

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**[s-straight; l-left; r-right; u-up; d-down; g-grounded amino acid (there is a pair of amino acids that serve as the point of reference)].