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amberequilibration.py
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amberequilibration.py
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# coding: utf-8
# Author: Julien Michel<br>
# Email: [email protected]
#
# # equilibration
#
# This notebook runs a 3 step equilibration using AMBER.
#
# TODO) Make this MD package agnostic
# In[1]:
import BioSimSpace as BSS
# In[2]:
node = BSS.Gateway.Node("A node to equilibrate a solvated molecule.")
# In[3]:
node.addAuthor(name="Julien Michel", email="[email protected]", affiliation="University of Edimnburgh")
node.setLicense("GPLv3")
# In[4]:
node.addInput("input", BSS.Gateway.FileSet(help="Topology and coordinate files describing the solvated system"))
node.addInput("output", BSS.Gateway.String(help="The root name of the output files."))
# In[5]:
node.addOutput("nodeoutput", BSS.Gateway.FileSet(help="The parameterised and solvated molecular system in AMBER format."))
# In[6]:
node.showControls()
# # Load input
# In[7]:
system = BSS.IO.readMolecules(node.getInput("input"))
# # Minimisation
# In[8]:
# Initialise a short minimisation protocol.
protocol = BSS.Protocol.Minimisation(steps=1000)
# In[9]:
process = BSS.Process.Amber(system, protocol, name="minimise")
# In[10]:
process.getConfig()
# In[11]:
process.start()
# In[12]:
process.wait()
# In[13]:
minimised = process.getSystem()
# # NVT equilibration (heat up to 300 K with positional restraints on non water molecules)
# In[14]:
# TODO Extend API so can restrain everything but water
# Use loop to run until target T achieved
protocol = BSS.Protocol.Equilibration(runtime=BSS.Types.Time(0.01, "nanosecond"),
temperature_start=BSS.Types.Temperature(0, "kelvin"),
temperature_end=BSS.Types.Temperature(300, "kelvin"),
restrain_backbone=True)
# In[15]:
process = BSS.Process.Amber(minimised, protocol, name="equilibrate-nvt")
# In[16]:
process.getConfig()
# In[17]:
process.start()
# In[18]:
process.wait()
# In[19]:
temps = process.getTemperature(time_series=True)
# In[20]:
# Generate a plot of volume vs temperature.
#plotT = BSS.Notebook.plot(process.getTime(time_series=True),
# temps, xlabel="Time (ns)", ylabel="Temperature (K)")
# In[21]:
nvt_equilibrated = process.getSystem()
# # NPT equilibration (300 K, no positional restraints)
# In[48]:
# TODO
# Use loop to run until target density achieved
# Allow setting of target pressure from constructor
protocol = BSS.Protocol.Equilibration(runtime=BSS.Types.Time(0.01, "nanosecond"),
temperature=BSS.Types.Temperature(300, "kelvin"),
ensemble="NPT")
# In[49]:
process = BSS.Process.Amber(nvt_equilibrated, protocol, name="equilibrate-npt")
# ## Override default protocol to wrap particle coordinates in minimum image
# In[50]:
config = process.getConfig()
print (config)
# In[51]:
config[-1] = "iwrap=1,"
config.append(' /')
# In[52]:
print(config)
# In[53]:
process.setConfig(config)
# In[54]:
process.start()
# In[55]:
process.wait()
# In[ ]:
#process.getDensity()
# In[56]:
vols = process.getVolume(time_series=True)
# In[57]:
# Generate a plot of volume vs temperature.
#plotV = BSS.Notebook.plot(process.getTime(time_series=True),
# vols, xlabel="Time (ns)", ylabel="Volume (A3^3)")
# In[58]:
npt_equilibrated = process.getSystem()
# # Terminate node
# In[59]:
node.setOutput("nodeoutput", BSS.IO.saveMolecules(node.getInput("output"), npt_equilibrated, ["rst7"]))
# In[60]:
node.validate()