def step_01(self, instance):
"""This steps does the trajectory simulation. First, the input files
are downloaded from a remote HTTP server. Next, NAMD reads the 'inp'
("input") file and simulates the trajectory. Finally, the output is
transferred back to the machine on which this script is executed.
"""
namd = Kernel(name="md.namd")
namd.core = 4
namd.arguments = ["eq{0}.inp".format(instance)]
namd.download_input_data = ["http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.pdb > complex.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.top > complex.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/cons.pdb > cons.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/eq0.inp > eq{0}.inp".format(instance)]
namd.download_output_data = "STDOUT > eq{0}.out".format(instance)
return namd
def step_01(self, instance):
"""This steps does the trajectory analysis, a.k.a free energy
calculation. First, the input files are downloaded from a remote
HTTP server. Next, MMPBSA reads the 'traj' ("trajectory") file and
carries out the analysis. Finally, the output is transferred back to
the machine on which this script is executed.
"""
mmpbsa = Kernel(name="md.mmpbsa")
mmpbsa.core = 4
mmpbsa.arguments = ["-i nmode.5h.py", "-cp com.top.2", "-rp rec.top.2", "-lp lig.top", "-y rep{0}.traj".format(instance)]
mmpbsa.download_input_data = ["http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/com.top.2 > com.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/rec.top.2 > rec.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/lig.top > lig.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/nmode.5h.py > nmode.5h.py",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/trajectories/rep1.traj > rep{0}.traj".format(instance)]
mmpbsa.download_output_data = "STDOUT > eq{0}.out".format(instance)
return mmpbsa
def step_01(self, instance):
"""This steps does the trajectory simulation. First, the input files
are downloaded from a remote HTTP server. Next, NAMD reads the 'inp'
("input") file and simulates the trajectory. Finally, the output is
transferred back to the machine on which this script is executed.
"""
namd = Kernel(name="md.namd")
namd.core = 4
namd.arguments = ["eq{0}.inp".format(instance)]
namd.download_input_data = [
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.pdb > complex.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.top > complex.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/cons.pdb > cons.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/eq0.inp > eq{0}.inp"
.format(instance)
]
namd.download_output_data = "STDOUT > eq{0}.out".format(instance)
return namd
def step_01(self, instance):
"""This steps does the trajectory analysis, a.k.a free energy
calculation. First, the input files are downloaded from a remote
HTTP server. Next, MMPBSA reads the 'traj' ("trajectory") file and
carries out the analysis. Finally, the output is transferred back to
the machine on which this script is executed.
"""
mmpbsa = Kernel(name="md.mmpbsa")
mmpbsa.core = 4
mmpbsa.arguments = [
"-i nmode.5h.py", "-cp com.top.2", "-rp rec.top.2", "-lp lig.top",
"-y rep{0}.traj".format(instance)
]
mmpbsa.download_input_data = [
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/com.top.2 > com.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/rec.top.2 > rec.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/lig.top > lig.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/nmode.5h.py > nmode.5h.py",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/trajectories/rep1.traj > rep{0}.traj"
.format(instance)
]
mmpbsa.download_output_data = "STDOUT > eq{0}.out".format(instance)
return mmpbsa
