- added input files for 2 peptides (1LE1, 1LY2) runs on matrix

- minor changes in makefile and test script

diff --git a/source/ga/Makefile b/source/ga/Makefile
index 13399f6..369fb85 100644 (file)
--- a/source/ga/Makefile
+++ b/source/ga/Makefile
@@ -1,5 +1,5 @@
 
-CC             := ifort
+FC             := ifort
 CFLAGS         := 
 
 BUILD_DIR      := build        
@@ -13,7 +13,7 @@ CLUSTER               := matrix
 all: checkdirs checktpl build/unresga
 
 build/unresga:GA.f
-       $(CC) $(CFLAGS) GA.f -o $@
+       $(FC) $(CFLAGS) GA.f -o $@
 
 
 checkdirs: $(BUILD_DIR)

diff --git a/source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl b/source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl
new file mode 100644 (file)
index 0000000..6fc5fce
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl
@@ -0,0 +1,14 @@
+1LE1 random parameters #1
+SEED=-6086648 RE pdbref refstr ONE_LETTER  rescale_mode=2 out1file extconf
+nstep=2000000  ntwe=10000 ntwx=10000 lang=0 tbf t_bath=300 tau_bath=1.0        &
+dt=0.10 reset_moment=1000 reset_vel=10000 damax=4.0 
+nrep=16 nstex=10000 tlist mlist traj1file rest1file sync nsyn=10000 tonly      &
+hremd={POPSIZE}
+ 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400
+   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
+{WEIGHTS}
+{PREFIX}.pdb
+22
+XNLYIQWLKDGGPSSGRPPPSX
+0
+0

diff --git a/source/ga/input-templates/matrix-2p/1L2Y_wham.tpl b/source/ga/input-templates/matrix-2p/1L2Y_wham.tpl
new file mode 100644 (file)
index 0000000..c980249
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/1L2Y_wham.tpl
@@ -0,0 +1,46 @@
+SEED=-3059743 n_ene=19 isampl=1 nq=1 classify pdbref einicheck=1               &
+rescale=2 ensembles=0 nslice=1 HAMIL_REP oneletter cxfile separate_parset      &
+nparmset={POPSIZE}
+nres=22 one_letter
+XNLYIQWLKDGGPSSGRPPPSX
+0
+{WEIGHTS}
+NT=16 replica
+NR=1 TEMP= 250.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 260.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 270.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 280.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 290.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 300.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 310.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 320.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 330.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 340.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 350.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 360.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 370.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 380.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 390.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 400.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+nfile_cx=1 rec_start=101   rec_end=200    totraj=256
+./{PREFIX}_mremd_MD000
+CUTOFF_UP=8.0 CUTOFF_LOW=4.0 NLEVEL=-2 PDBREF                                  &
+SPLIT_BET=1 NC_FRAC_HEL=0.7 NC_FRAC_BET=0.5 NC_FRAC_PAIR=0.5 NSHIFT_PAIR=3     &
+CONT_PAIR=1 NC_FRAC_PAIR=0.5 RMS_PAIR=0
+./{PREFIX}.pdb

diff --git a/source/ga/input-templates/matrix-2p/1LE1_mremd.tpl b/source/ga/input-templates/matrix-2p/1LE1_mremd.tpl
new file mode 100644 (file)
index 0000000..b36236a
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/1LE1_mremd.tpl
@@ -0,0 +1,14 @@
+1LE1 random parameters #1
+SEED=-6086648 RE pdbref refstr ONE_LETTER  rescale_mode=2 out1file extconf
+nstep=2000000  ntwe=10000 ntwx=10000 lang=0 tbf t_bath=300 tau_bath=1.0        &
+dt=0.10 reset_moment=1000 reset_vel=10000 damax=4.0 
+nrep=16 nstex=10000 tlist mlist traj1file rest1file sync nsyn=10000 tonly      &
+hremd={POPSIZE}
+ 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400
+   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
+{WEIGHTS}
+{PREFIX}.pdb
+14
+XSWTWENGKWTWKX
+0
+0

diff --git a/source/ga/input-templates/matrix-2p/1LE1_wham.tpl b/source/ga/input-templates/matrix-2p/1LE1_wham.tpl
new file mode 100644 (file)
index 0000000..f68f1e3
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/1LE1_wham.tpl
@@ -0,0 +1,46 @@
+SEED=-3059743 n_ene=19 isampl=1 nq=1 classify pdbref einicheck=1               &
+rescale=2 ensembles=0 nslice=1 HAMIL_REP oneletter cxfile separate_parset      &
+nparmset={POPSIZE}
+nres=14 one_letter
+XSWTWENGKWTWKX
+0
+{WEIGHTS}
+NT=16 replica
+NR=1 TEMP= 250.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 260.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 270.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 280.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 290.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 300.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 310.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 320.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 330.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 340.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 350.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 360.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 370.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 380.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 390.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+NR=1 TEMP= 400.0 FI=  0.00000   0.00000   0.00000   0.00000   0.00000
+KH=   0.00 Q0=0.00000
+nfile_cx=1 rec_start=101   rec_end=200    totraj=256
+./{PREFIX}_mremd_MD000
+CUTOFF_UP=8.0 CUTOFF_LOW=4.0 NLEVEL=-2 PDBREF                                  &
+SPLIT_BET=1 NC_FRAC_HEL=0.7 NC_FRAC_BET=0.5 NC_FRAC_PAIR=0.5 NSHIFT_PAIR=3     &
+CONT_PAIR=1 NC_FRAC_PAIR=0.5 RMS_PAIR=0
+./{PREFIX}.pdb

diff --git a/source/ga/input-templates/matrix-2p/opt.csh b/source/ga/input-templates/matrix-2p/opt.csh
new file mode 100755 (executable)
index 0000000..f8f14b5
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/opt.csh
@@ -0,0 +1,69 @@
+#!/bin/csh -f
+# Script to run the program zscorezi_MPI on linux with MPICH (parallel version).
+#
+
+echo "This job is running on host `hostname` "
+
+set DD =  /users/adam/UNRES/PARAM
+set BIN = /users/adam/ZSCOREZ/bin
+
+set POT = GB
+setenv POT GB
+
+setenv PREFIX zscore
+setenv SCRATCHDIR /tmp/`whoami`
+
+if ( ! -d $SCRATCHDIR ) then
+  mkdir $SCRATCHDIR 
+endif
+
+#hostname
+#ls -l /tmp
+
+#
+# Is the specified potential in the list of valid force fields?
+#
+if (($POT != "LJ") && ($POT != "LJK") && ($POT != "BP") && ($POT != "GB") \
+&& ($POT != "GBV") ) then
+  echo "Unknown potential type $POT"
+  exit(1)
+endif
+
+# 5/17/97 parameter file assignment was changed from link to SETENV statements
+#
+setenv BONDPAR $DD/bond_AM1.parm
+setenv THETPAR $DD/theta_abinitio.parm
+setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm
+#setenv BONDPAR $DD/bond.parm
+#setenv THETPAR $DD/thetaml.5parm
+#setenv ROTPAR $DD/scgauss.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR $DD/scinter_${POT}.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+
+# Set parallel environment, depending on job type (interactive or batch).
+
+set DEBUG = 0
+
+# Choose the sidechain contact function
+
+setenv CONTFUNC GB
+if (${CONTFUNC} == "GB") then
+  setenv SIDEP ${DD}/contact.3.parm
+else if (${CONTFUNC} == "SCDIST") then
+  setenv SIDEP ${DD}/cend.3.45.parm
+else if (${CONTFUNC} == "CEN") then
+  setenv SIDEP ${DD}/cen.parm
+else if (${CONTFUNC} == "ODC") then
+  setenv SIDEP ${DD}/odc.parm
+else if (${CONTFUNC} != "SIG") then
+  echo "Unknown sidechain contact function ${CONTFUNC}"
+  exit
+endif
+
+limit coredumpsize 0
+$BIN/zscorezMD_sccor-T-OPTERON-clust-sign-split $*

diff --git a/source/ga/input-templates/matrix-2p/start_all.pbs b/source/ga/input-templates/matrix-2p/start_all.pbs
new file mode 100755 (executable)
index 0000000..e859950
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/start_all.pbs
@@ -0,0 +1,27 @@
+#PBS -N single-test
+#PBS -q dque
+#PBS -l nodes=32:ppn=8
+#PBS -l walltime=1:00:00
+
+set NPROCS=`cat $PBS_NODEFILE | wc -l`
+
+cd $PBS_O_WORKDIR
+
+./unresga
+
+cat $PBS_NODEFILE|uniq > nody
+
+time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS -p4wd $PBS_O_WORKDIR  $PBS_O_WORKDIR/unres_p1.csh
+time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS -p4wd $PBS_O_WORKDIR  $PBS_O_WORKDIR/unres_p2.csh
+
+time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np 16 -p4wd $PBS_O_WORKDIR  $PBS_O_WORKDIR/wham_p1.csh
+time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np 16 -p4wd $PBS_O_WORKDIR  $PBS_O_WORKDIR/wham_p2.csh
+
+time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np 16 ./opt.csh
+
+set DATA=`date +%Y-%m-%d-%H%M%S`
+mkdir ceiksy-$DATA
+mv *.cx ceiksy-$DATA
+
+#mail -s "Scheraga - wyniki dla single-test sa dostepne" lightnir@gmail.com
+

diff --git a/source/ga/input-templates/matrix-2p/unres_p1.csh b/source/ga/input-templates/matrix-2p/unres_p1.csh
new file mode 100755 (executable)
index 0000000..5d5fc95
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/unres_p1.csh
@@ -0,0 +1,26 @@
+#!/bin/csh -f
+
+set DD = /users/czarek/UNRES/PARAM
+#-----------------------------------------------------------------------------
+setenv FGPROCS 0
+setenv POT GB
+setenv PREFIX 1LE1_mremd
+setenv OUT1FILE Y
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users/czarek/UNRES/NEW/bin/unres_Tc_procor_new_em64_nh_hremd.exe
+#-----------------------------------------------------------------------------
+setenv BONDPAR $DD/bond_AM1.parm
+setenv THETPAR $DD/theta_abinitio.parm
+setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR $DD/scinter_${POT}.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+setenv PATTERN $DD/patterns.cart
+#-----------------------------------------------------------------------------
+
+$UNRES_BIN $*
+

diff --git a/source/ga/input-templates/matrix-2p/unres_p2.csh b/source/ga/input-templates/matrix-2p/unres_p2.csh
new file mode 100755 (executable)
index 0000000..312bef9
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/unres_p2.csh
@@ -0,0 +1,26 @@
+#!/bin/csh -f
+
+set DD = /users/czarek/UNRES/PARAM
+#-----------------------------------------------------------------------------
+setenv FGPROCS 0
+setenv POT GB
+setenv PREFIX 1L2Y_mremd
+setenv OUT1FILE Y
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users/czarek/UNRES/NEW/bin/unres_Tc_procor_new_em64_nh_hremd.exe
+#-----------------------------------------------------------------------------
+setenv BONDPAR $DD/bond_AM1.parm
+setenv THETPAR $DD/theta_abinitio.parm
+setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR $DD/scinter_${POT}.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+setenv PATTERN $DD/patterns.cart
+#-----------------------------------------------------------------------------
+
+$UNRES_BIN $*
+

diff --git a/source/ga/input-templates/matrix-2p/unresga.inp b/source/ga/input-templates/matrix-2p/unresga.inp
new file mode 100644 (file)
index 0000000..870fdd2
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/unresga.inp
@@ -0,0 +1,7 @@
+pdb=1LE1.pdb 1L2Y.pdb
+alg=csa
+generations=5
+cicutoff=0.01
+population=8
+whamtemplate=1LE1_wham.tpl 1L2Y_wham.tpl
+mremdtemplate=1LE1_mremd.tpl 1L2Y_mremd.tpl

diff --git a/source/ga/input-templates/matrix-2p/wham_p1.csh b/source/ga/input-templates/matrix-2p/wham_p1.csh
new file mode 100755 (executable)
index 0000000..e8fcddc
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/wham_p1.csh
@@ -0,0 +1,66 @@
+#!/bin/csh -f
+#set echo
+# Script to run the program zscorezi_MPI on linux with MPICH (parallel version).
+#
+echo "This job is running on host `hostname` "
+
+set DD =  /users/adam/UNRES/PARAM
+set BIN = /users/adam/ZSCOREZ/bin
+
+set POT = GB
+setenv POT GB
+setenv SCRATCHDIR /tmp/`whoami`
+
+#
+# Przygotowanie i wyczyszczenie poletka 
+#
+if ( ! -d $SCRATCHDIR ) then
+ mkdir $SCRATCHDIR
+endif
+rm -f $SCRATCHDIR/*
+
+setenv PREFIX 1LE1_wham
+
+#
+# Is the specified potential in the list of valid force fields?
+#
+if (($POT != "LJ") && ($POT != "LJK") && ($POT != "BP") && ($POT != "GB") \
+&& ($POT != "GBV") ) then
+  echo "Unknown potential type $POT"
+  exit(1)
+endif
+
+# 5/17/97 parameter file assignment was changed from link to SETENV statements
+#
+setenv BONDPAR $DD/bond_AM1.parm
+setenv THETPAR $DD/theta_abinitio.parm
+setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR $DD/scinter_${POT}.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+setenv PATTERN $DD/patterns.cart
+# Define contact function for classification
+setenv CONTFUNC GB
+if (${CONTFUNC} == "GB") then
+  setenv SIDEP ${DD}/contact.3.parm
+else if (${CONTFUNC} == "SCDIST") then
+  setenv SIDEP ${DD}/cend.3.45.parm
+else if (${CONTFUNC} == "CEN") then
+  setenv SIDEP ${DD}/cen.parm
+else if (${CONTFUNC} == "ODC") then
+  setenv SIDEP ${DD}/odc.parm
+else if (${CONTFUNC} != "SIG") then
+  echo "Unknown sidechain contact function ${CONTFUNC}"
+  exit
+endif
+
+# Set parallel environment, depending on job type (interactive or batch).
+
+set DEBUG = 0
+
+limit coredumpsize 0
+$BIN/wham_multparm-hamrep-sep $*

diff --git a/source/ga/input-templates/matrix-2p/wham_p2.csh b/source/ga/input-templates/matrix-2p/wham_p2.csh
new file mode 100755 (executable)
index 0000000..e9081b3
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/wham_p2.csh
@@ -0,0 +1,66 @@
+#!/bin/csh -f
+#set echo
+# Script to run the program zscorezi_MPI on linux with MPICH (parallel version).
+#
+echo "This job is running on host `hostname` "
+
+set DD =  /users/adam/UNRES/PARAM
+set BIN = /users/adam/ZSCOREZ/bin
+
+set POT = GB
+setenv POT GB
+setenv SCRATCHDIR /tmp/`whoami`
+
+#
+# Przygotowanie i wyczyszczenie poletka 
+#
+if ( ! -d $SCRATCHDIR ) then
+ mkdir $SCRATCHDIR
+endif
+rm -f $SCRATCHDIR/*
+
+setenv PREFIX 1L2Y_wham
+
+#
+# Is the specified potential in the list of valid force fields?
+#
+if (($POT != "LJ") && ($POT != "LJK") && ($POT != "BP") && ($POT != "GB") \
+&& ($POT != "GBV") ) then
+  echo "Unknown potential type $POT"
+  exit(1)
+endif
+
+# 5/17/97 parameter file assignment was changed from link to SETENV statements
+#
+setenv BONDPAR $DD/bond_AM1.parm
+setenv THETPAR $DD/theta_abinitio.parm
+setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR $DD/scinter_${POT}.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+setenv PATTERN $DD/patterns.cart
+# Define contact function for classification
+setenv CONTFUNC GB
+if (${CONTFUNC} == "GB") then
+  setenv SIDEP ${DD}/contact.3.parm
+else if (${CONTFUNC} == "SCDIST") then
+  setenv SIDEP ${DD}/cend.3.45.parm
+else if (${CONTFUNC} == "CEN") then
+  setenv SIDEP ${DD}/cen.parm
+else if (${CONTFUNC} == "ODC") then
+  setenv SIDEP ${DD}/odc.parm
+else if (${CONTFUNC} != "SIG") then
+  echo "Unknown sidechain contact function ${CONTFUNC}"
+  exit
+endif
+
+# Set parallel environment, depending on job type (interactive or batch).
+
+set DEBUG = 0
+
+limit coredumpsize 0
+$BIN/wham_multparm-hamrep-sep $*

diff --git a/source/ga/input-templates/matrix-2p/zscore.tpl b/source/ga/input-templates/matrix-2p/zscore.tpl
new file mode 100644 (file)
index 0000000..1ccc44e
--- /dev/null
+++ b/source/ga/input-templates/matrix-2p/zscore.tpl
@@ -0,0 +1,135 @@
+iseed=3269 n_ene=19 nparmset={POPSIZE} out_newe
+mask_sc=0 mask_scp=1 mask_elec=1 mask_ang=1 mask_scloc=1 mask_tor=1            &
+mask_tord=1 mask_corrh=1 mask_corr5=0 mask_corr6=0 mask_el_loc=1               &
+mask_turn3=1 mask_turn4=1 mask_turn6=0 mask_vdwpp=1 mask_sccor=1
+wlow_sc=0.8 wlow_scp=0.0 wlow_elec=0.00 wlow_ang=0.00 wlow_scloc=0.00          &
+wlow_tor=0.0 wlow_tord=0.0 wlow_corrh=0.00 wlow_corr5=0.00 wlow_corr6=0.00     &
+wlow_sccor=0.0                                                                 &
+wlow_el_loc=0.00 wlow_turn3=0.00 wlow_turn4=0.00 wlow_turn6=0.00 wlow_vdwpp=0.0 
+wup_sc=1.2 wup_scp=5.0 wup_elec=5.0 wup_ang=5.00 wup_scloc=5.0                 &
+wup_tor=5.0 wup_tord=5.0 wup_corrh=5.0 wup_corr5=5.0 wup_corr6=5.0             &
+wup_el_loc=5.0 wup_turn3=5.0  wup_turn4=5.0 wup_turn6=5.0 wup_vdwpp=5.0        &
+wup_sccor=0.0
+mode=3 maxmin=10  maxfun=2000 opt_mode=0 tolf=1.0E-4 rtolf=1.0E-4 out_minim    &
+print_ini print_fin print_stat optimize_other read_stat=4 minimizer=sumsl      &
+rescale_mode=2
+mod_side
+end
+mod_fourier
+end
+mod_elec
+end
+mod_scp
+end
+{WEIGHTS}
+nprot=2
+{PREFIX01}
+rmscut=2.0 rmscut_gap=2.0 rkt=0.01 0.01 dkt=0.01 enecut=10000 enecut_min=10000 &
+enecut_max=20000 nbatch=1 nclass=2 nlevel=1
+id=coil nelem=1 mask=*.0.*
+id=native nelem=1  mask=*.1.*
+ngap_read=1 nT=13 beta=270 270 280 280 290 290 300 300 310 310 320 320 330 330 &
+340 340 345 345 350 350 360 360 370 370 380 380                                &
+hefac=10000 htfac=10000 helow=0 htlow=0
+nlev1=1 nlev2=1 level1=native level2=coil
+enegap=-2.0 -0.6   ewall=0.01                   !270
+enegap=-2.0 -0.6   ewall=0.01                   !280
+enegap=-2.0 -0.6   ewall=0.01                   !290
+enegap=-2.0 -0.6   ewall=0.01                   !300
+enegap=-2.0 -0.6   ewall=0.01                   !310
+enegap=-2.0 -0.6   ewall=0.01                   !320
+enegap=-2.0 -0.6   ewall=0.01                   !330
+enegap=-2.0 -0.6   ewall=0.01                   !340
+enegap=-0.5 0.5    ewall=0.01                   !345
+enegap=0.5 5.0     ewall=0.01                   !350
+enegap=0.5 5.0     ewall=0.01                   !360
+enegap=0.5 5.0     ewall=0.01                   !370
+enegap=0.5 5.0     ewall=0.01                   !380
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !270
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !280
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !290
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !300
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !310
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !320
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !330
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !340
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !345
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !350
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !360
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !370
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !380
+./{PARAM01}
+nres=14 one_letter
+XSWTWENGKWTWKX
+ 0
+PDBREF CAONLY SPLIT_BET=0 print_class nfrag=1
+CUTOFF_UP=6.0  CUTOFF_LOW=6.0  RMSUP_LIM=6.0  RMSUPUP_LIM=6.0  NFRAG=1         &
+FRAC_SEC=0.3
+npiece=1 n_shift1=3 n_shift2=3 rms=1 qcut=0.40 qwol=1 local=0 angcut=60.0      &
+elcont=0 sccont=0
+ifrag1=2  ifrag2=13
+./{PREFIX01}.pdb
+read_weights=1
+batch=1 class=all                                                              &
+qlow=0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.40 0.60 0.70 0.70 0.70          &
+ qup=0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.90 0.90 0.90 0.90 0.90          &
+wq=1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10       &
+1.0d10 1.0d10 1.0d10
+end
+{PREFIX02}
+rmscut=2.0 rmscut_gap=2.0 rkt=0.01 0.01 dkt=0.01 enecut=10000 enecut_min=10000 &
+enecut_max=20000 nbatch=1 nclass=2 nlevel=1
+id=coil nelem=1 mask=*.0.*
+id=native nelem=1  mask=*.1.*
+ngap_read=1 nT=13 beta=270 270 280 280 290 290 300 300 310 310 320 320 330 330 &
+340 340 345 345 350 350 360 360 370 370 380 380                                &
+hefac=10000 htfac=10000 helow=0 htlow=0
+nlev1=1 nlev2=1 level1=native level2=coil
+enegap=-2.0 -0.6   ewall=0.01                   !270
+enegap=-2.0 -0.6   ewall=0.01                   !280
+enegap=-2.0 -0.6   ewall=0.01                   !290
+enegap=-2.0 -0.6   ewall=0.01                   !300
+enegap=-2.0 -0.6   ewall=0.01                   !310
+enegap=-2.0 -0.6   ewall=0.01                   !320
+enegap=-2.0 -0.6   ewall=0.01                   !330
+enegap=-2.0 -0.6   ewall=0.01                   !340
+enegap=-0.5 0.5    ewall=0.01                   !345
+enegap=0.5 5.0     ewall=0.01                   !350
+enegap=0.5 5.0     ewall=0.01                   !360
+enegap=0.5 5.0     ewall=0.01                   !370
+enegap=0.5 5.0     ewall=0.01                   !380
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !270
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !280
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !290
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !300
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !310
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !320
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !330
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !340
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !345
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !350
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !360
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !370
+entshanwall=3.0e9 1.0e5  3.0e9  3.0e9  3.0e9  !380
+./{PARAM02}
+nres=22 one_letter
+XNLYIQWLKDGGPSSGRPPPSX
+ 0
+PDBREF CAONLY SPLIT_BET=0 print_class nfrag=1
+CUTOFF_UP=6.0  CUTOFF_LOW=6.0  RMSUP_LIM=6.0  RMSUPUP_LIM=6.0  NFRAG=1         &
+FRAC_SEC=0.3
+npiece=1 n_shift1=3 n_shift2=3 rms=1 qcut=0.40 qwol=1 local=0 angcut=60.0      &
+elcont=0 sccont=0
+ifrag1=2  ifrag2=13
+./{PREFIX02}.pdb
+read_weights=1
+batch=1 class=all                                                              &
+qlow=0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.40 0.60 0.70 0.70 0.70          &
+ qup=0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.90 0.90 0.90 0.90 0.90          &
+wq=1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10       &
+1.0d10 1.0d10 1.0d10
+end
+nthehel=25 ngahel=40 the0hel=70 dthehel=2 ga0hel=-100                          &
+nrbet=15 r0bet=3.0 nthebet=50 the0bet=60 dthebet=2 phialpha=60.0 delr=15.0     &
+delb=4.0 PHIALPHA_RIGHT=47.0 PHIALPHA_LEFT=44.0
+NGRIDT=400 T0=200 DELTAT=1

diff --git a/source/ga/tester.sh b/source/ga/tester.sh
index 8ac452f..253fab2 100755 (executable)
--- a/source/ga/tester.sh
+++ b/source/ga/tester.sh
@@ -6,7 +6,7 @@ if [ -d build ]; then
 fi
 make
 cd build
-cp -r ~/poligon/zero/* ./
+cp -r ~/poligon/first-step/* ./
 ./unresga
 
 echo ""