Thermodynamics(1) Manual Page

Name

Thermodynamics - Use the Transition-Tempered Orthogonal Space Random Walk algorithm to estimate a free energy.

Synopsis

Thermodynamics [-hovVy] [--iso] [--iW] [--mc] [--mcHW] [--meta] [--rn] [--ts] [--ac=<selection>] [--ac2=<selection>] [-b=Bussi] [--barInt=10] [--bpi=1000] [-C=10] [-d=1.0] [--dw=OFF] [-F=XYZ] [--firstDir=0] [-i=Verlet] [-k=1.0] [-l=-1] [--lf=91.0] [--lm=10.0] [--lw=0.0] [--maxAM=0.5] [--maxD=1.6] [--maxV=1.0] [--mcL=0.01] [--mcMD=100] [--mdE=FFX] [--minD=0.75] [-n=1000000] [--np=1] [-p=0] [-Q=1000] [-r=0.25] [--rsym=-1.0] [--ruc=-1.0] [--sf=1.0] [-t=298.15] [--tA=OST] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] [-w=10.0] [-z=100] [--bM=0.05[,0.05…]]… [--tp=4.0[,4.0…]]… [--tth=20*bias[,20*bias…]]… files…

Description

Use the Transition-Tempered Orthogonal Space Random Walk algorithm to estimate a free energy.

Options

-F, --fileFormat=XYZ: Choose file type to write [PDB/XYZ].
-h, --help: Print command help and exit.
-v, --verbose: Log additional information (primarily for MC-OST).
-V, --version: Print the Force Field X version and exit.

Dynamics Options

-b, --thermostat=Bussi: Thermostat: [Adiabatic / Berendsen / Bussi].
-d, --dt=1.0: Time discretization step in femtoseconds.
-i, --integrator=Verlet: Integrator: [Beeman / Respa / Stochastic / Verlet].
-k, --checkpoint=1.0: Interval in psec to write out restart files (.dyn, .his, etc).
--mdE, --molecularDynamicsEngine=FFX: Use FFX or OpenMM to integrate dynamics.
-n, --numberOfSteps=1000000: Number of molecular dynamics steps.
-o, --optimize: Optimize and save low-energy snapshots.
-r, --report=0.25: Interval in psec to report thermodynamics (psec).
-t, --temperature=298.15: Temperature (Kelvin).
-w, --write=10.0: Interval in psec to write out coordinates (psec).
-z, --trajSteps=100: Number of steps per MD cycle (--mdE = OpenMM only).

Monte Carlo Pressure Options

--barInt, --meanBarostatInterval=10: Sets the mean number of MD steps between barostat move proposals.
--bpi, --barostatPrintInterval=1000: Sets the number of Barostat MC cycles between print statements.
--iso, --isotropic: Restrict the MC Barostat to isotropic moves.
--maxAM, --maxAngleMove=0.5: Sets the width of proposed crystal angle moves (uniformly distributed) in degrees.
--maxD, --maxDensity=1.6: Specify the maximum density accepted by the MC Barostat (g/cc).
--maxV, --maxVolumeMove=1.0: Default width of proposed unit cell side length moves (uniformly distributed) in Angstroms.
--minD, --minDensity=0.75: Specify the minimum density accepted by the MC Barostat (g/cc).
-p, --npt=0: Specify use of a MC Barostat at the given pressure; the default 0 disables NPT (atm).

Random Unit Cell Options

--rsym, --randomSymOp=-1.0: Apply a random SymOp with translation range -X/2 .. X/2 (0 for random placement in the unit cell, negative for no SymOp)
--ruc, --randomUnitCell=-1.0: Apply random unit cell parameters to achieve the specified density (g/cc).

Alchemical Options

--ac, --alchemicalAtoms=<selection>: Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N].
-l, --lambda=-1: Initial lambda value.
--uc, --unchargedAtoms=<selection>: Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].

Alchemical Options for Dual and Quad Topologies

--ac2, --alchemicalAtoms2=<selection>: Specify alchemical atoms for the 2nd topology [ALL, NONE, Range(s): 1-3,6-N].
--np, --nParallel=1: Number of topologies to evaluate in parallel
--sf, --switchingFunction=1.0: Switching function to use for dual topology: options are TRIG, MULT, or a number (original behavior with specified lambda exponent)
--uaA, --unsharedA=-1: Unshared atoms in the A dual topology (e.g. 1-24.32-65).
--uaB, --unsharedB=-1: Unshared atoms in the B dual topology (e.g. 1-24.32-65).
--uc2, --unchargedAtoms2=<selection>: Specify atoms without electrostatics for the 2nd topology [ALL, NONE, Range(s): 1-3,6-N].

Thermodynamics Options

-Q, --equilibrate=1000: Number of equilibration steps before evaluation of thermodynamics.
--rn, --resetNumSteps: Ignore prior steps logged in .lam or similar files
--tA, --thermodynamicsAlgorithm=OST: Choice of thermodynamics algorithm. The default is OST, while FIXED runs MD at a fixed lambda value (e.g. BAR)

Orthogonal Space Tempering Options

--bM, --biasMag=0.05[,0.05…]: Orthogonal Space Gaussian bias magnitude (kcal/mol); RepEx OST uses a comma-separated list.
-C, --count=10: Time steps between MD Orthogonal Space counts.
--iW, --independentWalkers: Enforces that each walker maintains their own histogram.
--lw, --lambdaWriteOut=0.0: Only write out snapshots if lambda is greater than the value specified.
--meta, --metaDynamics: Use a 1D metadynamics style bias.
--tp, --temperingRate=4.0[,4.0…]: Tempering rate parameter in multiples of kBT; RepEx OST uses a comma-separated list.
--tth, --temperingThreshold=20*bias[,20*bias…]: Tempering threshold in kcal/mol; RepEx OST uses a comma-separated list.

Monte Carlo Orthogonal Space Tempering Options

--mc, --monteCarlo: Specify use of Monte Carlo OST
--mcHW, --mcHardWall: Monte Carlo OST hard wall constraint.
--mcL, --mcLambdaStdDev=0.01: Standard deviation for lambda move.
--mcMD, --mcMDSteps=100: Number of dynamics steps to take for each MD trajectory for Monte Carlo OST
--ts, --twoStep: MC Orthogonal Space sampling using separate lambda and MD moves.

Lambda Particle Options for MD-OST

--lf, --lambdaFriction=91.0: Friction on the lambda particle (1/psec).
--lm, --lambdaMass=10.0: Mass of the lambda particle (AMU).

Multiple Walker Options for MPI Simulations

--dw, --distributeWalkers=OFF: AUTO: Pick up per-walker configurations as [filename.pdb]_[num], or specify a residue to distribute on.
--firstDir=0: The first directory to use for multiple walker jobs.
-y, --synchronous: Walker communication is synchronous

Arguments

files…: The atomic coordinate file in PDB or XYZ format.