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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=1.0E-18] [--lm=1.0E-18] [--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=1.0E-18

Friction on the lambda particle.

--lm, --lambdaMass=1.0E-18

Mass of the lambda particle.

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.