Force Field XThermodynamics(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).