start .top7prep

prepare
 system top7_prep
 new_top new_seq
 center
 solvate cube 7.0
 write top7_em.rst
 write top7_em.pdb
end

#task prepare

md
 system top7_em
 sd 1000
end

#task md optimize

task shell "cp top7_em.qrs top7_md001.rst"

md
 system top7_md001
 isotherm 10.0 trelax 0.1 0.1
 isobar
 equil 0 data 10000
 print step 10 stat 1000
 record rest 1000
 cutoff 1.0
 cells 5 5 5
 load pairs 10
end

task md dynamics

task shell "cp top7_md001.rst top7_md002.rst"

md
 system top7_md002
 isotherm 50.0 trelax 0.1 0.1
 isobar
 equil 0 data 10000
 print step 10 stat 1000
 record rest 1000
 cutoff 1.0
 cells 5 5 5
 load pairs 10
end

task md dynamics

task shell "cp top7_md002.rst top7_md003.rst"

md
 system top7_md003
 isotherm 100.0 trelax 0.1 0.1
 isobar
 equil 0 data 10000
 print step 10 stat 1000
 record rest 1000
 cutoff 1.0
 cells 5 5 5
 load pairs 10
end

task md dynamics

task shell "cp top7_md003.rst top7_md004.rst"

md
 system top7_md004
 isotherm 200.0 trelax 0.1 0.1
 isobar
 equil 0 data 10000
 print step 10 stat 1000
 record rest 1000
 cutoff 1.0
 cells 5 5 5
 load pairs 10
end

task md dynamics

task shell "cp top7_md004.rst top7_md005.rst"

md
 system top7_md005
 isotherm trelax 0.1 0.1
 isobar
 equil 0 data 10000
 print step 10 stat 1000
 record rest 1000
 cutoff 1.0
 cells 5 5 5
 load pairs 10
end

task md dynamics

task shell "cp top7_md005.rst top7_md006.rst"

md
 system top7_md006
 isotherm trelax 0.1 0.1
 isobar
 pme grid 32 order 4
 equil 0 data 10000
 print step 10 stat 1000
 record rest 1000 coord 10
 cutoff 1.0
 cells 5 5 5
 load pairs 10
end

task md dynamics

analyze
 system top7_md007
 reference top7_md006.rst
 file top7_md006.trj
 select _CA
 essential
 project 1 vec1
end

task analyze
