.TH unresga 1    "September 26, 2011" "version 0.1" "USER COMMANDS"
.SH NAME
unresga \- finds optimal parameters for UNRES force-field by using genetic algorithm (GA)
.SH SYNOPSIS
.B unresga
.SH DESCRIPTION
This utility optimizes UNRES force-fields parameters (weights) by using genetic algorithm.
Curentely there are 19 parameters that can be optimized, altough not all of them are used (WLONG for instance).
These paremeters are defined in thó MD inputs as WLONG, WSCP, WELEC, WBOND, WANG, WSCLOC, WTOR, WTORD, WCORRH, WCORR4, WCORR5, WCORR6, WEL_LOC, WTURN3, WTURN4, WTURN6, WVDWPP, WHPB, WSCCOR.
The min and max boundries for these parameters are defined in the 
.I src/GA.inc
file.


.SH FILES
.IP unresga.inp 
This is the main configuration file 
.IP unresga.log 
This is the automaticly generated log file. Use it for troubleshooting.
.IP unresga.state 
state file used by the main program to manage input generation between MREMD, WHAM, ZSCORE steps. You shouldn't modify it unless something went terrible wrong and you realy know what you are doing...

.SH unresga.inp structure
The 
.I unresga.inp
file consists of 
.B key=value1 value2 ... valueX
entries. Key entries must be uppercase or lowercase, but not mixed-type. An example input file should look like this:   

.nf
pdb=1LE1.pdb 1L2Y.pdb
.br
alg=csa
.br
generations=50 
.br
cicutoff=5.0
.br
population=4
.br
whamtemplate=1LE1_wham.tpl 1L2Y_wham.tpl
.br
mremdtemplate=1LE1_mremd.tpl 1L2Y_mremd.tpl
.br
scripts=startwham.mat startmremd.mat
.fi

.IP PDB= 
Posible values are the reference PDB files used for calculations. At least one file should be specified. Maximum number of PDB files is set by variable maxnpdb in 
.I src/common.inc
(default 10)
.IP ALG=
Value defines witch algoritm should be used in genetic part. Values are: simple, better, betterv2, csa, cluster. 
.IP GENERATIONS=
Value sets maximum number of iterations for the genetic algorithm part.
.IP POPULATION=
Sets the size of bank population. Actual size of population is this value multiplied by value of the BANK_MULTIPLIER constant set in 
.I src/GA.inc
(default 4) 
.IP WHAMTEMPLATE=
Set the input template for generationg WHAM inputs. Number of templates should be equal to the number of PDB files.
.IP MREMDTEMPLATE=
Same as above but for MREMD inputs.  

.IP SCRIPTS=
Copy aditional files (shell scripts) for current input. This is obsolete and curentely disabled. 


.SH AUTHOR
Dawid Jagiela  (lightnir (at) chem.univ.gda.pl)