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|
#!/bin/bash
. ../MasterTest.sh
# Clean
CleanFiles hbond.in nhb.dat avghb.dat solvhb.dat solvavg.dat solutehb2.agr \
nbb.dat hbavg.dat solutehb.agr lifehb.gnu avg.lifehb.gnu max.lifehb.gnu \
crv.lifehb.gnu hb?.dat hbond.mol.dat mol.avg.dat \
ud.dat uh.dat ua.dat \
bridgeintermol.dat avgbridgeintermol.dat noacut.dat orthoavg.dat
INPUT="-i hbond.in"
# Solute-solute, series output, lifetime analysis
TestUU() {
UNITNAME='Solute Hbond test'
CheckFor netcdf
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
noprogress
parm ../DPDP.parm7
trajin ../DPDP.nc
hbond HB out nhb.dat avgout avghb.dat
hbond BB out nbb.dat @N,H,C,O series avgout hbavg.dat printatomnum
run
write solutehb.agr BB[solutehb] sort
runanalysis lifetime BB[solutehb] out lifehb.gnu window 10
EOF
RunCpptraj "$UNITNAME"
DoTest nhb.dat.save nhb.dat
DoTest avghb.dat.save avghb.dat
DoTest nbb.dat.save nbb.dat
DoTest hbavg.dat.save hbavg.dat
DoTest solutehb.agr.save solutehb.agr
DoTest lifehb.gnu.save lifehb.gnu
DoTest avg.lifehb.gnu.save avg.lifehb.gnu
DoTest max.lifehb.gnu.save max.lifehb.gnu
DoTest crv.lifehb.gnu.save crv.lifehb.gnu
fi
}
# Solute-solute, disk cache
TestUUcache() {
UNITNAME='Solute Hbond test with disk caching'
CheckFor netcdf notparallel
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
noprogress
parm ../DPDP.parm7
trajin ../DPDP.nc
usediskcache on
hbond BB @N,H,C,O series
run
write solutehb2.agr BB[solutehb] sort
EOF
RunCpptraj "$UNITNAME"
DoTest solutehb.agr.save solutehb2.agr
fi
}
# Solute-Solvent test
TestUV() {
UNITNAME='Solute-solvent hbond test'
CheckFor netcdf maxthreads 10
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm ../tz2.ortho.parm7
trajin ../tz2.ortho.nc
hbond hb out solvhb.dat avgout solvavg.dat :1-13 solventacceptor :WAT@O solventdonor :WAT \
solvout solvavg.dat bridgeout solvavg.dat
EOF
RunCpptraj "$UNITNAME"
DoTest solvhb.dat.save solvhb.dat
DoTest solvavg.dat.save solvavg.dat
fi
}
# Imaged hbond test
TestImage() {
UNITNAME='Hbond with imaging'
CheckFor maxthreads 1
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm strip.4lztSc_nowat.parm7
trajin strip.4lztSc.rst7
hbond donormask :3@ND2 acceptormask :1@O avgout hb1.dat image
hbond donormask :2@ND2 acceptormask :4@O avgout hb2.dat image
EOF
RunCpptraj "$UNITNAME"
DoTest hb1.dat.save hb1.dat
DoTest hb2.dat.save hb2.dat
fi
}
# Nointramol test
TestNointramol() {
UNITNAME='Hbond, no intramolecular hydrogen bonds test'
CheckFor netcdf maxthreads 10
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm ../FtuFabI.NAD.TCL.parm7
trajin ../FtuFabI.NAD.TCL.nc
hbond IntraMol out hbond.mol.dat
hbond NoIntraMol out hbond.mol.dat nointramol avgout mol.avg.dat
EOF
RunCpptraj "$UNITNAME"
DoTest hbond.mol.dat.save hbond.mol.dat
DoTest mol.avg.dat.save mol.avg.dat
fi
}
# Solute specified donor mask.
SpecifiedSoluteMask() {
UNITNAME='Hbond, specified solute masks'
CheckFor netcdf
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm ../DPDP.parm7
trajin ../DPDP.nc
hbond UDmask donormask @N= avgout ud.dat
hbond UHmask donormask @N&!:PRO,NHE donorhmask @H avgout uh.dat
hbond UAmask acceptormask @O avgout ua.dat
EOF
RunCpptraj "$UNITNAME"
DoTest ud.dat.save ud.dat
DoTest uh.dat.save uh.dat
DoTest ua.dat.save ua.dat
fi
}
NoAngleCut() {
UNITNAME='Hbond, no angle cutoff test'
CheckFor netcdf
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm ../DPDP.parm7
trajin ../DPDP.nc
hbond BB donormask :2-6@N acceptormask :9-13@O angle -1.0 dist 2.9 avgout noacut.dat
EOF
RunCpptraj "$UNITNAME"
DoTest noacut.dat.save noacut.dat
fi
}
BridgeIntermol() {
UNITNAME='Hbond, Bridge nointramol test'
CheckFor netcdf maxthreads 2
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm ../dna30.parm7
trajin ../Test_AutoImage/split.duplex.nc
hbond hb out bridgeintermol.dat avgout avgbridgeintermol.dat :1-60 \
solventacceptor :WAT@O solventdonor :WAT nointramol image
EOF
RunCpptraj "$UNITNAME"
DoTest bridgeintermol.dat.save bridgeintermol.dat
DoTest avgbridgeintermol.dat.save avgbridgeintermol.dat
fi
}
TestImageOrtho() {
UNITNAME='Hbond, orthogonal imaging'
CheckFor netcdf
if [ $? -eq 0 ] ; then
cat > hbond.in <<EOF
parm ../tz2.ortho.parm7
trajin ../tz2.ortho.nc
#trajin temp.nc
center :1-13 point 9.3 21.3 35.7
image :WAT
hbond hb image \
:1-13 solventacceptor :WAT@O solventdonor :WAT \
avgout orthoavg.dat \
solvout orthoavg.dat \
bridgeout orthoavg.dat
EOF
RunCpptraj "$UNITNAME"
DoTest solvavg.dat.save orthoavg.dat
fi
}
TestUU
TestUUcache
TestUV
TestNointramol
SpecifiedSoluteMask
NoAngleCut
BridgeIntermol
TestImage
TestImageOrtho
EndTest
exit 0
|
