Cli
schemas.workflow.amber.cli.AMBER_CLI_MAPPING = {'mdin': 'i', 'mdout': 'o', 'mdinfo': 'inf', 'prmtop': 'p', 'inpcrd': 'c', 'refc': 'refc', 'mtmd': 'mtmd', 'mdcrd': 'x', 'inptraj': 'y', 'mdvel': 'v', 'mdfrc': 'frc', 'mden': 'e', 'restrt': 'r', 'cpin': 'cpin', 'cprestrt': 'cprestart', 'cpout': 'cpout', 'cein': 'cein', 'cerestrt': 'cerestrt', 'ceout': 'ceout', 'evbin': 'evbin', 'suffix': 'suffix'}
module-attribute
¶
Maps keys from AmberCLIBase to Amber command-line options.
schemas.workflow.amber.cli.AmberCLIBase
¶
Bases: BaseModel, YamlIO, Render
cein = None
class-attribute
instance-attribute
¶
Sander option: -cein
input redox state definitions
ceout = None
class-attribute
instance-attribute
¶
Sander option: -ceout
output redox state data saved over trajectory
cerestrt = None
class-attribute
instance-attribute
¶
Sander option: -cerestrt
redox state definitions, final redox states for restart (same format as cein)
compute_platform = 'pmemd'
class-attribute
instance-attribute
¶
cpin = None
class-attribute
instance-attribute
¶
Sander option: -cpin
input protonation state definitions
cpout = None
class-attribute
instance-attribute
¶
Sander option: -cpout
output protonation state data saved over trajectory
cprestrt = None
class-attribute
instance-attribute
¶
Sander option: -cprestart
protonation state definitions, final protonation states for restart (same format as cpin)
evbin = None
class-attribute
instance-attribute
¶
Sander option: -evbin
input input for EVB potentials
inpcrd = 'mol.inpcrd'
class-attribute
instance-attribute
¶
Sander option: -c
Path to file containing input initial coordinates and (optionally) velocities and periodic box size.
inptraj = None
class-attribute
instance-attribute
¶
Sander option: -y
input coordinate sets in trajectory format, when imin=5 or 6
mdcrd = None
class-attribute
instance-attribute
¶
Sander option: -x
output coordinate sets saved over trajectory
mden = None
class-attribute
instance-attribute
¶
Sander option: -e
output extensive energy data over trajectory (not synchronized with mdcrd or mdvel)
mdfrc = None
class-attribute
instance-attribute
¶
Sander option: -frc
output force sets saved over trajectory
mdin = 'md.in'
class-attribute
instance-attribute
¶
Sander option: -i
Path to input file for controlling AMBER calculations and operations. Options
specified in AmberInputsBase should be in this file.
Below is a non-working example of what this file should look like.
mdinfo = 'md.info'
class-attribute
instance-attribute
¶
Sander option: -inf
Path to store the latest
mdout and other
simulation progress information. An example is shown below.
NSTEP = 494000 TIME(PS) = 2008.000 TEMP(K) = 301.01 PRESS = 0.0
Etot = -103688.2116 EKtot = 19750.7918 EPtot = -123439.0034
BOND = 691.6081 ANGLE = 1937.7561 DIHED = 1279.1292
UB = 0.0000 IMP = 0.0000 CMAP = 142.8106
1-4 NB = 795.8815 1-4 EEL = 10392.2564 VDWAALS = 18105.7369
EELEC = -156784.1822 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 317340.9390
Density = 1.0364
Ewald error estimate: 0.8100E-04
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps: 500000 | Completed: 494000 ( 98.8%) | Remaining: 6000
|
| Average timings for last 25500 steps:
| Elapsed(s) = 59.89 Per Step(ms) = 2.35
| ns/day = 73.58 seconds/ns = 1174.27
|
| Average timings for all steps:
| Elapsed(s) = 1142.43 Per Step(ms) = 2.31
| ns/day = 74.72 seconds/ns = 1156.31
|
|
| Estimated time remaining: 13.9 seconds.
------------------------------------------------------------------------------
mdout = 'md.out'
class-attribute
instance-attribute
¶
Sander option: -o
Output user readable state info and diagnostics. -o stdout will send output to
stdout (i.e., the terminal) instead of to a file. This stream will contain the
following information.
Characteristics of the Amber release.
-------------------------------------------------------
Amber 22 PMEMD 2022
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 22
| Compiled date/time: Thu Apr 14 14:06:37 2022
File paths.
File Assignments:
| MDIN: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| MDOUT: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| INPCRD: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| PARM: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| RESTRT: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| REFC: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| MDVEL: mdvel
| MDEN: mden
| MDCRD: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| MDINFO: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
|LOGFILE: logfile
| MDFRC: mdfrc
Then it will provide any notes and information about the chosen methods and system.
Afterwords, system information will be printed every
ntpr steps.
NSTEP = 500 TIME(PS) = 1021.000 TEMP(K) = 300.64 PRESS = 0.0
Etot = -103950.9351 EKtot = 19726.5940 EPtot = -123677.5291
BOND = 650.1569 ANGLE = 1869.0536 DIHED = 1260.6252
UB = 0.0000 IMP = 0.0000 CMAP = 155.1250
1-4 NB = 787.8972 1-4 EEL = 10500.5192 VDWAALS = 18651.1452
EELEC = -157552.0512 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 317418.4248
Density = 1.0361
Ewald error estimate: 0.1408E-04
------------------------------------------------------------------------------
The meaning of each term is below for convenience. You can find more information in the Amber manual.
NSTEP: Current step number.TIME(PS): Cumulative simulation time in picoseconds. The previous simulation time is included here if the simulation is a restart.TEMP(K): Instantaneous system temperature in Kelvin.PRESS: System pressure.Etot: Total energy as the sum of kinetic and potential energies.EKtot: Total kinetic energy.EPtot: Total potential energy.BOND: Sum of bond energies.ANGLE: Sum of angle energies.DIHED: Sum of dihedral energies.UB: Urey-Bradley energy term in the CHARMM force field.IMP: Improper energy term as in the CHARMM force field.CMAP: Correction map for dihedral energies first introduced in CHARMM in the extended in Amber's ff19SB (replaces cosine-based \(\phi\)/\(\psi\) dihedral terms in ff14SB).1-4 NB: 1-4 non-bonded (i.e., van der Waal) energy between atoms separated by three consecutive bonds. These interactions scale unlike the standard terms, so they are treated separately.1-4 EEL: 1-4 electrostatic energy between atoms separated by three consecutive bonds. These interactions scale unlike the standard terms, so they are treated separately.VDWAALS: van der Waals energy.EELEC: Electrostatic energy.EHBOND: Depreciated hydrogen bonding contributions.RESTRAINT: Energy of anyntrconstraints.EKCMT: ?VIRIAL: ?VOLUME: System volume in Å3.Density: System density in g/cm3.
mdvel = None
class-attribute
instance-attribute
¶
Sander option: -v
output velocity sets saved over trajectory
mtmd = None
class-attribute
instance-attribute
¶
Sander option: -mtmd
input (optional) containing list of files and parameters for targeted MD to multiple targets
prmtop = 'mol.prmtop'
class-attribute
instance-attribute
¶
Sander option: -p
Path to a file containing input molecular topology, force field, periodic box type, atom and residue names.
refc = None
class-attribute
instance-attribute
¶
Sander option: -ref
input (optional) reference coords for position restraints; also used for targeted MD
restrt = None
class-attribute
instance-attribute
¶
Sander option: -r
output final coordinates, velocity, and box dimensions if any - for restarting run
suffix = None
class-attribute
instance-attribute
¶
Sander option: -suffix
output this string will be added to all unspecified output files that are printed (for multisander runs, it will append this suffix to all output files)
render(with_newlines=False)
¶
Render the bash command to run an Amber simulation.