{
'protein':{
#####
####
###
##
#
'tags':['aamd','protein'],
'script':'protein.py',
'params':'parameters.py',
'extensions':[],
'settings':"""
step: protein # name of the folder is s01-protein
force field: charmm27 # which gromacs-standard force-field to use (see pdb2gmx list)
water: tip3p # which water model (another question from pdb2gmx)
equilibration: nvt-short,nvt,npt # which equilibration step to use (must have `input-name-in.mdp` below)
pdb source: 1yrf # PDB code for download. overrides the start structure
start structure: none # path to PDB structure or None to use a single PDB in inputs
protein water gap: 3.0 # Angstroms distance around the protein to remove water
water buffer: 1.2 # distance (nm) of solvent to the box wall
solvent: spc216 # starting solvent box (use spc216 from gromacs share)
ionic strength: 0.150 # desired molar ionic strength
cation: NA # name of the cation for neutralizing the system
anion: CL # name of the anion for neutralizing the system
#---INTEGRATOR PARAMETERS generated via parameters.py
mdp_specs:| {
'group':'aamd',
'mdps':{
'input-em-steep-in.mdp':['minimize'],
'input-em-cg-in.mdp':['minimize',{'integrator':'cg'}],
'input-md-nvt-eq-in.mdp':['nvt-protein','nvt-protein',{'nsteps':10000}],
'input-md-nvt-short-eq-in.mdp':['nvt-protein-short',{'nsteps':10000}],
'input-md-npt-eq-in.mdp':['npt-protein',{'nsteps':10000}],
'input-md-in.mdp':{'nsteps':100000},
},
}
"""},
'generate_charmm_landscape':{
#####
####
###
##
#
#
'tags':['aamd','landscape'],
'params':'@bilayers/parameters.py',
'extensions':[
'@charmm/landscape.py'],
'quick':"""
from amx import *
init()
write_charmm_landscape()
""",
'settings':"""
landscape at: @charmm/landscape.json
lipids: ['DOPC','DOPS','PI2P','CHL1','DOPE','POPC']
""",},
'bilayer_protein_topology_only':{
#####
####
###
##
#
'tags':['aamd','protein'],
'script':'protein-topology-only.py',
'params':None,
'extensions':[],
'settings':"""
step: protein # name of the folder is s01-protein
force field: charmm27 # which gromacs-standard force-field to use (see pdb2gmx list)
water: tip3p # which water model (another question from pdb2gmx)
"""},
'trialanine-demo':{
#####
####
###
##
#
'metarun':[
{'step':'protein','do':'protein','settings':""""""},
{'quick':'vmd_protein','settings':"""
step: v01-look
video name: video
view mode: video
#---video settings
max frames: 300 # aim for this many frames in the unbroken trajectory
video size: 30 # size in megabytes (requires ffmpeg 2-pass encoding)
duration: 0.0 # desired duration (requires ffmpeg)
webm: True # make a webm copy as well
#---resolution
viewbox: (800,800) # pixels in the VMD viewer (must match the resolution proportions)
resolution: (2400,1800) # snapshot and video resolution
which view: xview # camera direction
scale: scale by 1.75 # zoom factor (may require some tuning)
#---recipes set the aesthetics of the rendering
recipe collection: video aamd atomistic bilayer protein
#---align the protein
backbone align name: "name CA"
#---custom selections (see lib_vmdmake for details)
selections:| [{'basic_residues':'protein and (resname HIS or resname ARG or resname LYS)',
'smooth':True,'style':'licorice','goodsell':True},
][1:0]
#---^^^ customizations turned off if the list is sliced over 1:0"!
#---note: do not use smooth on some items but not others (induces a non-physical asynchronicity)
#---note: SEE lib_vmdmake.py and the vmdmake documentation for more details
""",
'jupyter_coda':"""
%%HTML
<video width="100%" controls>
<source src="./v01-look/video.webm">
</video>
"""}]},
}
