Fork me on GitHub

Thermodynamics(1)

Synopsis

Thermodynamics [-hovVy] [--iso] [--iW] [--mc] [--mcHW] [--meta] [--rn] [--rNEQ] [--ts] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<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] [--nEQ=100] [--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].
--acRes, --alchemicalResidues=<selection>
Specify alchemical residues by chain and residue number [A4,B21]
-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].
--acRes2, --alchemicalResidues2=<selection>
Specify alchemical residues by chain and residue number for the 2nd topology [A4,B21]
--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

--nEQ, --nonEquilibriumSteps=100
Sets the number of non-equilibrium lambda steps.
-Q, --equilibrate=1000
Number of equilibration steps before evaluation of thermodynamics.
--rn, --resetNumSteps
Ignore prior steps logged in .lam or similar files.
--rNEQ, --reverseNonEquilibrium
Run non-equilibrium dynamics from L=1 to L=0.
--tA, --thermodynamicsAlgorithm=OST
Choice of thermodynamics algorithm [OST, FIXED, or NEQ].

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.