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MCCCS Towhee (towhee_input Version 3.1.x)

 

 

 Overview
    This section covers the variables that are set in the towhee_input file Version 3.1.x. Each variable is listed along with its type (logical, character, integer, or double precision). towhee_input is the main input file for Towhee and is generally the only file that needs to be edited on a regular basis. It has a regimented style to the input. The variables are described here in the order they appear in this file. Please look at one of the example files (available with the code package) for the precise file format.
Bug reports / feature enhancements for 3.1.x versions
  • 3.1.1: Fixed a minor bug in checkhmatrix that caused a divide by zero core dump when the box dimensions went exactly to zero during an attempted volume move.
  • 3.1.0: Added the ldftfld which controls whether the classical density functional code Tramonto is called to compute a solvation free energy. Tramonto is not (yet) available to the general public. Modified the Makefile so it recompiles the entire code upon any change to the Makefile. In order to compile a serial version of the code (the only version currently possible in the code release) you now must type 'make serial' instead of just typing 'make'. Added a solvation energy to the list of energies. Added the fielddft.F subroutine.
towhee_input file differences from version 3.0.x
  • ldftfld was added. Set this variable to false unless you are one of the select few trying out the combined version of Towhee and Tramonto.
Variable explanations for towhee_input
    inputformat (character string)
    • 'Towhee' : reads in the input variables following the format for Towhee. This is the format that is described in this file.
    • 'LAMMPS' : reads in the input variables from the lammps_input and lammps_data files. Outputs files suitable for use with Towhee.
    • 'Quest' : reads in the input variables from the quest_input file. Outputs files suitable for use with Towhee.
    temperature (double precision)
    • The temperature in Kelvin.
    pressure (double precision)
    • The external pressure in kPa. This in only used if lnpt = .true., but you have to list a value regardless.
    nmolty (integer)
    • The total number of molecule types in the simulation. This must be less then or equal to NTMAX (see preproc.h).
    nmolectyp (integer)
    • The number of molecules of each type (listed sequentially on a single line). This variable was formerly known as moltyp.
    numboxes (integer)
    • The number of simulation boxes in the system. This value must be less than or equal to MAXBOXES (set in preproc.h). Note that many of the variables below depend upon numboxes as you will have to provide information for each box (such as box lengths).
    lcycles (logical)
    • .true. if nstep is the number of cycles, where a cycle is nchain Monte Carlo moves (nchain is the number of molecules in the system).
    • .false. if nstep is the number of Monte Carlo moves.
    nstep (integer)
    • The number of Monte Carlo steps to perform. If lcycles = .true. then each step is a cycle, otherwise each step is a single move.
    printfreq (integer)
    • The step frequency for outputting information about the system to stdout (fort.6). The information is the number of Monte Carlo steps performed thus far during the run, the total energy in each box, the x-box length of each box, the pressure of each box, and the number of molecules of each type in each box. This variable was formerly known as iprint
    blocksize (integer)
    • The size of the blocks for computing block averages. If you want this to be meaningful then blocksize should divide cleanly into nstep. The quantities that are averaged (in each simulation box) are the specific density, the pressure, all of the energy terms, the chemical potential of each molecule type, number density of each molecule type, and the mole fractions. This variable was formerly known as iblock
    moviefreq (integer)
    • The step frequency for outputting the system conformations to the towhee_movie file. This file is analyzed after the run using the analyze_movie.F routine to compute a variety of distribution functions. This file can get pretty big if you output frequently so be careful if you have a limited amount of hard disk space available. This variable was formerly known as imovie
    backupfreq (integer)
    • The step frequency for writing a file named towhee_backup that is suitable for use as a restart file. It overwrites the previous version of towhee_backup each time so it does not take up much space. Typically I set backupfreq so that I get around 10 backups during a run. For more information about restart files look at the manual entries for towhee_initial, towhee_backup, and towhee_final. This variable was formerly known as ibackup
    loutpdb (logical)
    • .true. if you wish to output Protein Data Bank (pdb) files for each simulation box at the end of the run. These files are named box_xx.pdb where xx is the simulation box number.
    • .false. if you do not want to output pdb files.
    loutdft (logical)
    • .true. if you wish to output files for use with the Tramonto classical density functional theory code. This outputs dft_surfaces.dat and dft_decode.dat. See the Tramonto code for information on what these files mean.
    • .false. if you do not want to output dft files.
    loutlammps (logical)
    • .true. if you wish to output files for use with the LAMMPS massively parallel molecular dynamics code. This outputs lammps_input and lammps_data# where the number is each of the simulation box numbers. See the LAMMPS documentation for more information on how to read in these files.
    • .false. if you do not want to output LAMMPS files.
    pressurefreq (integer)
    • The step frequency for computing the pressure in each simulation box. Be aware that computing the pressure is a fairly expensive task (especially for large systems) so if you don't really care about the computed pressure then it will pay to set pressurefreq to a high value. This variable formerly known as iratp
    trmaxdispfreq (integer)
    • The step frequency for updating the maximum translational (atom and center-of-mass) and rotational displacements. They are adjusted to try and achieve the target acceptance rates (see tatraa, tatrac, and tarot). It is a good idea to do this fairly frequently at the start of the simulation (every step or every 10 steps) in order to get good values for the maximum displacements. Once the acceptance rates are near their desired values I typically set trmaxdispfreq to do 10 updates during a run. This variable formerly known as iratio
    volmaxdispfreq (integer)
    • The step frequency for updating the maximum volume displacements. They are adjusted to try and achieve the target acceptance rates (see tavol). It is a good idea to do this fairly frequently at the start of the simulation (every few steps) in order to get good values for the maximum displacements. Once the acceptance rates are near their desired values I typically set volmaxdisp to do 10 updates during a run. This variable formerly known as iratv
    ffnumber (integer)
    • 0: uses the force field information that is built into the towhee program.
    • 1 or more: reads the force field information from the file(s) listed in the ff_filename.
    ff_filename (formatted character*70)
      This variable is only listed if ffnumber is not zero
    • A list of the filenames (one per line) that contain the force field information.
    potentyp (integer)
    • potentyp = 0: 12-6 Lennard-Jones van der Waals potential.
        • If the two atoms are separated by more than 3 bonds, or are on different molecules then
        Unonbond = 4 * nbcoeff(1) * [ (nbcoeff(2)/r)^12 - (nbcoeff(2)/r)^6 ]
        else if the two atoms are separated by exactly 3 bonds then
        Unonbond = 4 * nbcoeff(3) * [ (nbcoeff(4)/r)^12 - (nbcoeff(4)/r)^6 ]
    • potentyp = 1: 9-6 Lennard-Jones van der Waals potential
        • If the two atoms are separated 3 or more bonds, or are on different molecules then
        Unonbond = nbcoeff(2) * [ 2*(nbcoeff(1)/r)^9 - 3*(nbcoeff(1)/r)^6 ]
    • potentyp = 2: Exponential-6 van der Waals potential
        • If the two atoms are separated by more than 3 bonds, or are on different molecules then
        Unonbond = nbcoeff(1)/r^6 + nbcoeff(2) * exp[nbcoeff(3)*r]
    • potentyp = 3: Hard Sphere potential
        • If the two atoms are separated by more than 3 bonds, or are on different molecules then
        Unonbond = Infinity if r <= nbcoeff(1), or 0 otherwise
    • potentyp = -3: Repulsive Sphere potential. Added to towhee in version 1.4.6. This is used to help setup and equilibrate a hard sphere system where it is sometimes challenging to create an initial conformation with no overlaps. Use the -3 option to equilibrate until the nonbonded potential energy is 0.0, and then switch back to the normal hard sphere potential.
        • If the two atoms are separated by more than 3 bonds, or are on different molecules then
        Unonbond = 1d5 + 1d5 * (nbcoeff(1)^2 - r^2) if r <= nbcoeff(1), or 0 otherwise
    • potentyp = 4: Exponential plus 12-6 Lennard-Jones van der Waals potential
        • If the two atoms are separated by more than 3 bonds, or are on different molecules then
        Unonbond = nbcoeff(1)/r^6 + nbcoeff(2)/r^12 + nbcoeff(3)*exp[nbcoeff(4)*r]
    mixrule (integer)
    • mixrule = 0: Lorentz-Berthelot (arithmetic mean of sigma, geometric mean of epsilon) mixing rules. Only valid for potentyp = 0.
    • mixrule = 1: Geometric (geometric mean of sigma and epsilon) mixing rules. Only valid for potentyp = 0.
    • mixrule = 2: Compass (sixth order combination of sigma and epsilon) mixing rules. Only valid for potentyp = 1.
    • mixrule = 3: Gromos (geometric mean of sigma and epsilon with some special cases) mixing rules. Only valid for potentyp = 0.
    • mixrule = 4: Explicit (defined in ffnonbond.F) mixing rules. Only valid for potentyp = 2 or potentyp = 4.
    • mixrule = 5: Hard sphere (arithmetic mean of sigmas) mixing rules. Only valid for potentyp = 3.
    lshift (logical)
    • .true. if you want the nonbonded van der Waals potential to be shifted so that it is zero at the cutoff.
    • .false. if you do not want to shift the nonbonded van der Waals potential.
    ltailc (logical)
    • .true. if you want to apply analytical tail corrections for the portion of the van der Waals potential that is past the cutoff. Note that you cannot have a shifted potential and tail corrections at the same time.
    • .false. if you do not want analytical tail corrections for van der Waals.
    rmin (double precision)
    • A hard inner cutoff that can speed computation for Lennard-Jones systems, and is required to avoid the potential hitting infinity for exponential repulsion systems which also contain point charges. This should be set smaller than the smallest radius of any atom. Generally I set this to 0.5 or 1.0 Angstroms.
    rcut (double precision)
    • The van der Waals potential cutoff in Angstroms.
    rcutin (double precision)
    • The inner nonbonded cutoff used in configurational-bias Monte Carlo moves. This dual-cutoff method can speed configurational-bias computations by at least a factor of 2, without affecting the acceptance rate. The inner cutoff is used during the growth procedure, and the full potential is calculated at the end of the move and everything is fixed up in the acceptance criteria. I typically set this to 5 Angstroms for noncoulombic simulations, and to 10 Angstroms for coulombic simulations.
    lcoulomb (logical)
    • .true. if you want to use point charges in the simulation. If you are using point charges then the Ewald sum handles the long range corrections. Note that you can essentially disable the Ewald sum by setting both kalp and kmax to zero.
    • .false. if you do want to use point charges.
    kalp (double precision)
    • Value used in the Ewald sum to compute alpha. If you set kalp and kmax both to zero then you will effectively disable the Ewald sum. The actual Ewald sum alpha term is equal to kalp divided by the shortest box length. The recommended value for kalp is 5.6.
    kmax (integer)
    • Maximum number of inverse space vectors to use in any dimension for the Ewald sum. Recommended value of this parameter is 5. If you want to set this to a larger value to may have to increase VECTORMAX (see preproc.h). Note that you can effectively disable the Ewald sum by setting both kalp and kmax to zero.
    dielect (double precision)
    • The dielectric constant used when computing coulombic interactions. Generally this should be set to 1.0 as the solvated system will act as the screening that the dielectric constant is intended to represent. If you are performing a simulation without any solvent (for example a protein without the water) you might want to set the dielectric constant to represent the missing solvent.
    nhrdfld (integer)
    • Number of hard walls you wish to include in the simulation. As this is not typically used, it has a slightly different input style from normal. If nhrdfld = 0 then none of the hrd* variables are required in the input file. Otherwise for next nhrdfld lines each line should contain the values for hrdbox(ifield), hrdxyz(ifield), hrdcen(ifield), hrdrad(ifield) where those variables have the following meanings.
    • hrdbox (integer)
      • This is the number of the simulation box which contains this hard wall. Must range from 1 to numboxes.
    • hrdxyz (integer)
      • 1: hard wall is perpendicular to the x-axis (in the yz plane)
      • 2: hard wall is perpendicular to the y-axis (in the xz plane)
      • 3: hard wall is perpendicular to the z-axis (in the xy plane)
    • hrdcen (double precision)
      • Position of the center of the hard wall. Must be between 0.0 and the box length of the axis that is perpendicular to the wall.
    • hrdrad (double precision)
      • Radius of the hard wall. The wall will exclude all atoms whose centers are within this radius regardless of the potentyp or any of the atom parameters. Yes I know this is a strange cd way to run a hard wall. The wall is felt through the periodic boundaries.
    nljfld (integer)
    • Number of 9-3 Lennard-Jones walls you wish to include in the simulation. As this is not typically used, it has a slightly different input style from normal. If nljfld = 0 then none of the ljf* variables are required in the input file. Otherwise for next nljfld lines each line should contain the values for ljfbox(ifield), ljfxyz(ifield), ljfcen(ifield), ljfsig(ifield), ljfeps(ifield) ,ljfcut(ifield), and ljfdir(ifield) where those variables have the following meanings.
    • ljfbox (integer)
      • This is the number of the simulation box which contains this Lennard-Jones wall. Must range from 1 to numboxes.
    • ljfxyz (integer)
      • 1: Lennard-Jones wall is perpendicular to the x-axis (in the yz plane)
      • 2: Lennard-Jones wall is perpendicular to the y-axis (in the xz plane)
      • 3: Lennard-Jones wall is perpendicular to the z-axis (in the xy plane)
    • ljfcen (double precision)
      • Position of the center of the Lennard-Jones wall. Must be between 0.0 and the box length of the axis that is perpendicular to the wall.
    • ljfsig (double precision)
      • Sigma parameter for the 9-3 Lennard-Jones wall.
    • ljfeps (double precision)
      • Epsilon parameter for the 9-3 Lennard-Jones wall. All atoms in the system interact with the wall via the potential U = sqrt(2/5) ljfeps [ (1/5) (ljfsig/r)^9 - (3/2) (ljfsig/r)^3 ] regardless of the potentyp and parameters of each atom. Yes I know this is a strange way to run a 9-3 Lennard-Jones wall, but I don't use it much.
    • ljfcut (double precision)
      • The distance beyond which the wall-atom interactions are not computed. This potential is cut, not shifted, and never has tail corrections no matter how lshift and ltailc are set.
    • ljfdir (integer)
      • -1: Atoms only interact with the "left" face of this wall. This extends through the periodic boundary.
      • 1: Atoms only interact with the "right" face of this wall. This extends through the periodic boundary.
    nlragfld (integer)
    • Number of Raghavan et al. style 111 metal walls you wish to include in the simulation. Note that all of the field variables have a slightly different input style from normal. If nragfld = 0 then none of the rag* variables are required in the input file. Otherwise for next nragfld lines each line should contain the values for ragbox(ifield), ragxyz(ifield), ragcen(ifield), ragcut(ifield), ragdir(ifield) , and raglat(ifield) where those variables have the following meanings.
    • ragbox (integer)
      • This is the number of the simulation box which contains this Raghavan wall. Must range from 1 to numboxes.
    • ragxyz (integer)
      • 1: Raghavan wall is perpendicular to the x-axis (in the yz plane)
      • 2: Raghavan wall is perpendicular to the y-axis (in the xz plane)
      • 3: Raghavan wall is perpendicular to the z-axis (in the xy plane)
    • ragcen (double precision)
      • Position of the center of the Raghavan wall. Must be between 0.0 and the box length of the axis that is perpendicular to the wall.
    • ragcut (double precision)
      • The distance beyond which the Raghavan wall-atom interactions are not computed. This potential is cut, not shifted, and never has tail corrections no matter how lshift and ltailc are set.
    • ragdir (integer)
      • -1: Atoms only interact with the "left" face of this wall. This extends through the periodic boundary.
      • 1: Atoms only interact with the "right" face of this wall. This extends through the periodic boundary.
    • raglat (double precision)
      • The lattice spacing of the metal atoms in the 111 wall. This is the "a" parameter in the Raghavan wall potential.
    ldftfld (logical)
    • .true. if you are using the classical density functional theory code Tramonto to compute a solvation free energy.
    • .false. otherwise
    linit (logical)
    • .true. if you are starting the simulation and wish to generate the positions of all of the atoms, assign initial box lengths and maximum displacements.
    • .false. if you want to continue the simulation by reading in box lengths, maximum displacements, and coordinates from towhee_initial.
    initstyle (integer)
      One line for each simulation box in the system. Each line contains a value for each molecule type.
    • 0: A template for this molecule type is created using configurational-bias. This template is then replicated throughout the simulation box to generate an initial configuration.
    • 1: A template for this molecule type is read from towhee_template. This template is then replicated throughout the simulation box to generate an initial configuration.
    • 2: The coordinates for each atom are read from towhee_coords. This is useful if you are starting from a different file format (such as pdb), or have another code for building an initial configuration.
    hmatrix (double precision)
    • The initial box dimensions (Angstroms) for the three vectors that describe the simulation box. There are nine entries (3 for each of the 3 vectors) in total for each simulation box. These are listed one vector at a time, with the three numbers which make up each vector listed on the same line. Note that the coordinate system you choose does not have to be orthogonal, but it must follow the right hand rule. The three vectors must also all be at least 45 degrees apart. Note that if you wish to use a rectangular box then only the diagonal elements of hmatrix will be non-zero, and these will be equal to the boxlengths in the x, y, and z dimensions.
    initmol (integer)
    • The initial number of each type of molecule in each box (one line per box).
    inix, iniy, iniz (integer)
    • The initial number of molecules in each direction in each box. The product of inix*iniy*iniz must be greater than or equal to the initial number of molecules in that box (the sums of initmol). While these are labeled x, y, and z they actually correspond to the three coordinate vectors.
    inimix (integer)
      One line for each simulation box in the system.
    • -1: molecules are initially placed in each box in alternating order.
    • 0: molecules are initially placed in each box in random order.
    • 1: molecules are initially placed in each box order. Thus all molecules of type 1 are placed in a box before any molecules of type 2. If you are using initstyle = 2 then this is the only valid option and the other options will be reset to this option by the code.
    lnpt (logical)
    • .true. if you want the volume moves to be performed in an exchange with an external pressure bath (isobaric isothermal ensemble or isobaric-isothermal Gibbs ensemble).
    • .false. if you do want the total volume of the system to be conserved. In the case of a multi-box simulation this exchanges volume between pairs of boxes (canonical Gibbs ensemble), in a single box case no volume moves are allowed (canonical ensemble).
  • Note: the pm* variables are used to determine which move type to perform every time we want to do a Monte Carlo move. A move is selected by choosing a random number between 0.0 and 1.0 and then going down the list of pm* until you find one which has a value higher than the random number. At least one of the variables must be set to 1.0. A similar procedure is performed when we want to determine which boxes or molecule types to perform the selected move upon. These are done using the pm**pr and pm**mt arrays.
    • pmvol (double precision)
    • Probability of performing a volume move. If (lnpt = .true.) then a single box is selected and it exchanges volume with an external pressure bath (see pressure). If (lnpt = .false. and numboxes > 1) a pair of boxes are selected and volume is exchanged between them.
    pmvlpr (double precision)
    • Probability of performing a volume move on a particular box, or box pair. All of these variables are listed on a single line If (lnpt = .true.) then a value of pmvlpr is listed for each box. If (lnpt = .false.) then a value is listed for each pair of simulation boxes where the pairs are ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes).
    rmvol (double precision)
    • The initial volume maximum displacement. If this is an isobaric-isothermal ensemble (lnpt = .true.) then this is the initial maximum volume displacement (cubic Angstroms) in each box. If this is the canonical Gibbs ensemble (lnpt = .false. and numboxes > 1 ) then this is the maximum displacement (logarithmic space) for each pair of boxes. As the simulation progresses, these values will be updated for each box, or each pair of boxes (see iratv).
    tavol (double precision)
    • The target acceptance rate for the volume move. Must be a value between 0.0 and 1.0. The volume displacement (rmvol) is periodically adjusted (see iratv) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    pmcell (double precision)
    • Probability of performing a unit cell adjustment move. If (lnpt = .true.) then a single box is selected and a single hmatrix element is changed. This results in a volume exchange with a fictional external pressure bath (see pressure). If (lnpt = .false. and numboxes > 1) a pair of boxes are selected. One of the boxes is then selected according to the pmcellpt variable and a single hmatrix element is changed in that box. This results in a change of volume for the first box which is countered by isotropically changing the volume in the second box.
    pmcellpr (double precision)
    • Probability of performing a unit cell adjustment move on a particular box, or box pair. All of these variables are listed on a single line If (lnpt = .true.) then a value of pmvlpr is listed for each box. If (lnpt = .false.) then a value is listed for each pair of simulation boxes where the pairs are ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes).
    pmcellpt (double precision)
    • Probability of selecting the first box of the pair as the box to perform the non-isotropic volume move upon, while its partner undergoes an isotropic volume move. This variable is only meaningful if (lnpt=.false.). Note that you can choose to perform the non-isotropic volume move always on the same box and this might be useful if you are doing a solid-vapor equilibria calculation.
    rmcell (double precision)
    • The initial unit cell adjustment maximum displacement. In all cases, this is the maximum amount (in Angstroms) that a single element of the hmatrix can change in a single unit cell move. Note, the in the canonical Gibbs ensemble case it is possible for the isotropic box to undergo an hmatrix change that is larger than this value as that box simply makes up for the volume change caused by the non-isotropic adjustment in the first box. As the simulation progresses, these values are updated for each box with a frequency controlled by iratv.
    tacell (double precision)
    • The target acceptance rate for the unit cell adjustment move. Must be a value between 0.0 and 1.0. The unit cell displacement (rmcell) is periodically adjusted (see iratv) to yield this acceptance rate. I typically use a value of 0.5.
    pm2boxrbswap (double precision)
    • Probability of performing a rotational-bias interbox molecule transfer move. This move takes a molecule out of one box and tries to place it in another box. The molecule is grown using nchoice attempted different orientations and position (of the center-of-mass) for the new molecule.
    pm2rbswmt (double precision)
    • Probability of performing a rotational-bias interbox molecule transfer move on each type of molecule in the system.
    pm2rbswpr (double precision)
    • Probability of performing a rotational-bias interbox molecule transfer move between each pair of boxes in the system. The box pairs are ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes).
    pm2boxcbswap (double precision)
    • Probability of performing a configurational-bias interbox molecule transfer move. This move takes a molecule out of one box and tries to place it in another box. The molecule is grown using coupled-decoupled configurational-bias Monte Carlo. This variable was formerly known as pmswap
    pm2cbswmt (double precision)
    • Probability of performing a configurational-bias interbox molecule transfer move on each type of molecule in the system. This variable was formerly known as pmswmt.
    pm2cbswpr (double precision)
    • Probability of performing a configurational-bias interbox molecule transfer move between each pair of boxes in the system. The box pairs are ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes). This variable was formerly known as pmswpr
    pm1boxcbswap (double precision)
    • Probability of performing an intrabox configurational-bias molecule transfer move. This move takes a molecule out of one box and tries to place it back into the same box. The molecule is grown using coupled-decoupled configurational-bias Monte Carlo This variable was formerly known as pmiswp
    pm1bcbswmt (double precision)
    • Probability of performing an intrabox configurational-bias molecule transfer move on each type of molecule in the system. This variable was formerly known as pmismt
    pmavb1 (double precision)
    • Probability of performing an aggregation volume bias move of type 1, as described in Chen and Siepmann 2001. This is useful for forming and destroying clusters in simulations with molecules that tend to aggregate together.
    pmavb1mt (double precision)
    • Probability of performing an aggregation volume bias move of type 1 where a molecule of a certain type is moved. This is an array with one element for each molecule type.
    pmavb1ct (double precision)
    • Probability of performing an aggregation volume bias move of type 1 where the molecule target is of a certain type. The molecule that is moved is chosen according to pmavb1mt and then the type of molecule that is used as a reference for determining the inner and outer regions is found using this variable. This is a two dimensional array and uses one line of text for each type of molecule in the system.
    avb1rad (double precision)
    • The radius used to define the inner and outer volumes in the aggregation volume bias move of type 1. The distance is specified in Angstroms and must be greater than zero, but less than or equal to rcut.
    pmcb (double precision)
    • Probability of performing a molecule regrowth move on a molecule without regard to which box the molecule is currently located in. This move chooses a molecule of the appropriate type at random, selects an atom of the molecule at random, and then regrows the molecule either entirely (if a random number < pmall) or in all directions except for one. The molecule is regrown using configurational-bias.
    pmcbmt (double precision)
    • Probability of performing a molecule regrowth on each type of molecule in the system.
    pmall (double precision)
    • pmall is the probability that a molecule regrowth move will regrow the entire molecule. This is listed for each molecule type in the simulation.
    pmback (double precision)
    • Probability of performing configurational-bias fixed-endpoint regrowth of a portion of the protein backbone. This selects an atom along the peptide backbone, chooses another backbone atom that is connected by three bonds to the first atom, and then regrows all of the atoms inbetween these two atoms.
    pmbkmt (double precision)
    • Probability of performing a backbone regrowth move on each type of molecule in the system.
    pmplane (double precision)
    • Probability of performing a plane shift move. This move displaces all of the molecules whose center of mass lies in a plane of width planewidth. A new trial position for the center of the plane of atoms is generated uniformly across the available plane.
    pmplanebox (double precision)
    • Probability of performing a plane shift in each of the simulation boxes. List one value for each simulation box. At least one of the boxes must have a value of 1.0d0.
    planewidth (double precision)
    • The width of the plane for the plane shift move. Any molecule whose center of mass is within a plane of this thickness (whose position is chosen uniformly along one axis) will move during the plane shift move. The value of planewidth must be greater than 0.0d0 and less than the shortest boxlength.
    pmrow (double precision)
    • Probability of performing a row shift move. This move displaces all of the molecules whose center of mass lies in a row of diameter rowwidth. A new trial position for the center of the row of atoms is generated uniformly across the available row.
    pmrowbox (double precision)
    • Probability of performing a row shift in each of the simulation boxes. List one value for each simulation box. At least one of the boxes must have a value of 1.0d0.
    rowwidth (double precision)
    • The width of the plan for the row shift move. Any molecule whose center of mass is within a row of this thickness (whose position is chosen uniformly along one axis) will move during the row shift move. The value of rowwidth must be greater than 0.0d0 and less than the shortest boxlength.
    pmtraat (double precision)
    • Probability of performing a single-atom translation move a molecule without regard to which box the molecule is currently located in. This move chooses a molecule of the appropriate type at random, selects an atom of the molecule at random, chooses the x,y, or z direction at random, and then attempts to displace the atom a random distance between -rmtraa and +rmtraa in that direction.
    pmtamt (double precision)
    • Probability of performing a single-atom translation move on each type of molecule in the system.
    rmtraa (double precision)
    • The initial Atom-translation maximum displacement (Angstroms) for all molecules types in all boxes. As the simulation progresses, these values will be updated independently to give the desired acceptance rate for each molecule type in each dimension of each box (see iratio).
    tatraa (double precision)
    • The target acceptance rate for the atom translation move. Must be a value between 0.0 and 1.0. The maximum atom translational displacement (rmtraa) is periodically adjusted (see iratio) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    pmtracm (double precision)
    • Probability of performing a center-of-mass translation move a molecule without regard to which box the molecule is currently located in. This move chooses a molecule of the appropriate type at random, chooses the x,y, or z direction at random, and then attempts to displace the entire molecule a random distance between -rmtrac and +rmtrac in that direction.
    pmtcmt (double precision)
    • Probability of performing a center-of-mass translation move on each type of molecule in the system.
    rmtrac (double precision)
    • The initial Center-of-mass translation maximum displacement (Angstroms) for all molecule types in all boxes. As the simulation progresses, these values will be updated independently to give the desired acceptance rate for each molecule type in each dimension of each box (see iratio).
    tatrac (double precision)
    • The target acceptance rate for the center-of-mass translation move. Must be a value between 0.0 and 1.0. The maximum center-of-mass translational displacement (rmtrac) is periodically adjusted (see iratio) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    pmrotate (double precision)
    • Probability of performing a rotation about the center-of-mass move for a molecule without regard to which box the molecule is currently located in. This move chooses a molecule of the appropriate type at random, chooses the x,y, or z direction at random, and then attempts to rotate the entire molecule about an x,y, or z axis that runs through the center-of-mass a random number of radians between -rmrot and +rmrot.
    pmromt (double precision)
    • Probability of performing a rotation move on each type of molecule in the system.
    rmrot (double precision)
    • The initial molecular rotation maximum displacement (radians) for all molecule types in all boxes. As the simulation progresses, these values will be updated independently to give the desired acceptance rate for each molecule type about each axis of each box (see iratio).
    tarot (double precision)
    • The target acceptance rate for the rotation move. Must be a value between 0.0 and 1.0. The rotation displacement (rmrot) is periodically adjusted (see iratio) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    cbstyle (integer)
    • cbstyle = 0: When performing a configurational-bias move, generate trial bond lengths, bending angles, and dihedral angles according to the true, ideal probability distribution. This is the method described in Martin and Siepmann 1999
    • cbstyle = 1: When performing a configurational-bias move, generate trial bond lengths, bending angles, and dihedral angles according to a different probability density and then fix this up in the acceptance rules. This work is still in progress and is not yet published.
    nchoi1 (integer)
    • This is the number of trial positions that are sampled for the first atom inserted during a configurational-bias molecule exchange move (see pmswp and pmiswp). I typically use a value of 10. The value must be less than or equal to NCHMAX (see preproc.h).
    nchoi (integer)
    • This is the number of trial positions that are sampled for all atoms except for the first atom inserted during a configurational-bias molecule exchange move (see pmswp and pmiswp). This is used for all atoms in a configurational-bias regrowth move. I typically use a value of 10. The value must be less than or equal to NCHMAX (see preproc.h).
    nchtor (integer)
    • This is the number of trial dihedral angles that are sampled during configurational-bias moves. I typically use a value in the range 100 to 360. The value must be less than or equal to NCHTOR_MAX (see preproc.h).
    nchconn (integer)
    • This is the number of trial dihedral angles that are sampled during configurational-bias moves when we have grown the molecule such that we need to connect back up with atoms that already exist. This is needed in order to regrow cyclic molecules, and also could be used to regrow the interiors of large molecules (not yet implemented). I typically use a value in the range 200 to 360. The value must be less than or equal to NCHTOR_MAX (see preproc.h).
    nchbna (integer)
    • This is the number of trial angles that are sampled during configurational-bias moves when we are selecting the iugrow-iufrom-iuprev angle. I typically use a value of 1000 for cbstyle of 0, and 100 for cbstyle of 1.
    nchbnb (integer)
    • This is the number of trial angles that are sampled during configurational-bias moves when we are selecting the rotation about a cone of one of the iugrow angles relative to the others. I typically use a value of 1000 for cbstyle of 0, and 100 for cbstyle of 1.
    nchvib (integer)
    • This is the number of trial bond lengths that are sampled during configurational-bias moves when we are growing atoms. I typically use a value of 1000 for cbstyle 0 and 100 for cbstyle 1, unless I am using a fixed-bond length force field, in which case you might as well just use 1.
    vibrang (double precision, double precision)
    • This is the range of bond lengths to sample via configurational-bias Monte Carlo. The range is expressed as a fraction of the equilibrium bond length for the lower bound and the upper bound. I usually values of 0.85 and 1.15 for cbstyle 1, and the values have no meaning for cbstyle 1.
    sdevtor (double precision)
    • This is the standard deviation of a gaussian distribution that is used to sample dihedral angles [on 0,360] during a configurational-bias regrowth for cbstyle 1. Specify a value in degrees. Right now I am using a value of 20.0. If cbstyle is not 1 then this value is not used in the code, but must still be entered into the input file.
    sdevbena (double precision)
    • This is the standard deviation of a gaussian distribution that is used to generate trials for the part A bending angles [on 0,180] during a configurational-bias regrowth for cbstyle 1. Specify a value in degrees. Right now I am using a value of 10.0. If cbstyle is not 1 then this value is not used in the code, but must still be entered into the input file.
    sdevbenb (double precision)
    • This is the standard deviation of a gaussian distribution that is used to generate trials for the part B bending angles [on 0,360] during a configurational-bias regrowth for cbstyle 1. Specify a value in degrees. Right now I am using a value of 20.0. If cbstyle is not 1 then this value is not used in the code, but must still be entered into the input file.
    sdevvib (double precision)
    • This is the standard deviation of a gaussian distribution that is used to sample bond lengths during a configurational-bias regrowth for cbstyle 1. Specify a value in Angtroms. Right now I am using a value of 0.1. If cbstyle is not 1 then this value is not used in the code, but must still be entered into the input file.
  • The final section of towhee_input contains the information that is used to construct the forcefield for the molecule types in the system. There are three different ways to set up this section that depend on inpstyle. The first way requires an explicit declaration of the entire force field and while it allows the most flexibility, is quite a burden to set up for any molecule with more than 10 atoms. The second option is an automated builder which works for any molecule, so long as the force field you wish to use has been implemented properly into the code. The final option is a builder for proteins, or other amino acid sequences. The choice of inpstyle determines what happens below it so all of the remaining variables are described in each case of inpstyle.
    • inpstyle (integer)
    • 0: Explicit declaration of all terms of the force field that describes this molecule type. This is the hardest way to set up the molecule information, but it also allows for the most flexibility. I do not recommend using this option unless it is not possible to use the more sophisticated options for the molecule of interest.
      • nunit (integer)
      • The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX (see preproc.h).
      nmaxcbmc (integer)
      • The maximum number of atoms to regrow during a configurational-bias regrowth. Generally I set this to the same value as nunit, but occasionally a molecule is so large that almost none of the moves which regrow large portions are accepted. In this case I set nmaxcbmc to be around 1/2 of nunit so that only smaller regrowths are performed.
      lpdb (logical)
      • .true. if you want to input information about the pdb (protein data bank) atom name, amino acid number, amino acid name. This information is needed in order to use the cartoon feature of certain pdb viewers (such as Rasmol).
      • .false. if you don't need that feature. A pdb file will still be output using the atom types defined in ffnonbond so you can still view the system, you just can not use the cartoon feature.

      The variables listed immediately below (unit through improper) are listed as a group for each atom in the molecule. Thus, you input all of the information about the first atom before you list information for the subsequent atoms.

      unit (integer), ntype (integer), qqatom (double precision)
      • unit is the number of the atom in order starting from atom number 1. This is only used to help the user keep track of the molecule as they are building it in the input file. If the unit number listed in towhee_input does not match the running total of unit numbers in Towhee then the code will stop with an error message.
      • ntype is the integer that ffnonbond uses to determine the force field parameters. You will need to look in ffnonbond.F in order to find the number that you wish to use.
      • qqatom is the charge on this atom. This value is not used (but must still be input) if lcoulomb is false.
      pdbname (character), aminonum (integer), aminoshort (character)
        These variables only need to be listed if lpdb = .true.
      • pdbname: A four letter/number string that is output in the pdb file. The precise spacing is important if you want to get most pdb viewers to recognize the atoms as the pdb file is extremely specific.
      • aminonum: The number of each amino acid starting from the N-terminus.
      • aminoshort: The three letter code for each amino acid, or other group (such as caps on the C or N termini).
      vibration
        invib (integer)
        • The first line under the vibration heading is the number of atoms that are bonded to the current atom. Must be a number between 0 and NNBOND (see preproc.h).
        ijvib (integer), itvib (integer)
        • The next invib lines underneath the vibration heading are a list of the bond partner and bond force field number (see ffbond.F) for the invib atoms that are bonded to the current atom. Thus if you have 4 vibrations the next 4 lines will list the bond partner and bond force field number for each bond.
      bending
        inben (integer)
        • The first line under the bending heading is the number of bond bending angles that terminate at the current atom. You must list all bond bending angles which have the current atom at one of the ends, but you do not list bond bending angles which contain the current atom in the center. Must be a number between 0 and NNBOND*(NNBOND-1) (see preproc.h).
        ijben2 (integer), ijben3(integer), itben (integer)
        • The next inben lines underneath the bending heading are a list of the other atoms in the bond bending angle and the bond bending angle force field number (see ffangle.F) for the inben angles that contain the current atom at one of the ends. The format for listing the angle is to consider the current atom in the first position of an angle between atoms current-ijben2-ijben3 so you only need to list atoms ijben2 and ijben3 and the bending type on each line, where there is one angle per line of towhee_input.
      torsion
        intor (integer)
        • The first line under the torsion heading is the number of dihedral angles (regular torsions) that terminate at the current atom. You must list all regular torsion angles which have the current atom at one of the ends, but you do not list regular torsion angles which contain the current atom in the center. Must be a number between 0 and NNBOND*(NNBOND-1)*(NNBOND-1) (see preproc.h).
        ijtor2 (integer), ijtor3(integer), ijtor4 (integer), ittor (integer)
        • The next intor lines underneath the torsion heading are a list of the other atoms in the regular torsion angle and the torsion force field number (see fftorsion.F) for the intor torsions that contain the current atom at one of the ends. The format for listing the regular torsion angle is to consider the current atom in the first position of a dihedral between atoms current-ijtor2-ijtor3-ijtor4 so you only need to list atoms ijtor2, ijtor3, and ijtor4 and the torsion type on each line, where there is one regular torsion per line of towhee_input.
      angle-angle
        inaa (integer)
        • The first line under the angle-angle heading is the number of angle-angle terms which have their shared central atom located at the current atom. You must list all angle-angle terms which have the current atom at the shared central position, but you do not list angle-angle terms which contain the current atom at one of the ends. Must be a number between 0 and (NNBOND*(NNBOND-1))/2 (see preproc.h).
        ijaa0 (integer), ijaa1(integer), ijaa2 (integer), itaa (integer)
        • The next inaa lines underneath the angle-angle heading are a list of the other atoms in the angle-angle term and and the angle-angle force field number (see ffangang.F) for the inaa angle-angle terms that contain the current atom at the shared central atom. The format for listing the regular torsion angle is to consider the current atom as the central shared atom in the angle-angle term between the angles ijaa0-current-ijaa1 and ijaa0-current-ijaa2. Each angle-angle term is listed on one line according to the format ijaa0, ijaa1, ijaa2 and itaa (the angle-angle type).
      improper torsion
        inimprop (integer)
        • The first line under the improper heading is the number of improper torsions (any form) which have the central atom located at the current atom. You must list all improper torsions which have the current atom at the central position, but you do not list improper torsions which contain the current atom at one of the ends. Must be a number between 0 and ((NNBOND-1)*(NNBOND-2))/2 (see preproc.h).
        ijimprop2 (integer), ijimprop3(integer), ijimprop4 (integer), itimprop (integer)
        • The next inimprop lines underneath the improper torsion heading are a list of the other atoms in the improper torsion and the improper force field number (see ffimproper.F) for the inimprop improper torsions that contain the current atom at the central atom. There are currently three different forms of improper torsions, and these forms are specified in the force field (either in ffimproper.F or in towhee_ff). In all cases, the three atoms must all be bound to the current atom.
          • Form 1: Amber / Stereo Improper. This type of improper torsion works by computing the dihedral angle between the planes formed by the atoms ijimprop2-current-ijimprop3 and ijimprop2-current-ijimprop4. This was originally used as a means to enforce planarity, but is also useful for enforcing stereochemistry. The format for the stereo improper torsion is to list atoms ijimprop2, ijimprop3, and ijimprop4 and the torsion type (itimprop) on each line, where there is one improper torsion per line of towhee_input.
          • Form 2: Charmm / Simple Out-of-Plane. The format for listing the simple out-of-plane improper torsion is to consider the current atom in the first position of a dihedral between atoms current-ijimprop2-ijimprop3-ijimprop4 so you only need to list atoms ijimprop2, ijimprop3, and ijimprop4 and the torsion type on each line, where there is one improper torsion per line of towhee_input.
          • Form 3: Averaged Out-of-Plane. The format for listing the averaged out-of-plane improper torsion is identical to the simple out-of-plane. The only difference is that the dihedral used is not just the current-ijimprop2-ijimprop3-ijimprop4, but is instead an average of the following three angles: current-ijimprop2-ijimprop3-ijimprop4; current-ijimprop3-ijimprop4-ijimprop2; current-ijimprop4-ijimprop2-ijimprop3.
      This is the end of the section that is repeated for each atom for inpstyle=0

       

    • 1: Polypeptide builder which sets up everything using buildprot and assemble routines. This sets up everything for proteins from a list of the amino acids. This routine also could be used to build polymers, but I have not yet coded in any non-peptide monomers. I am working on some documentation of the currently available monomers, but until that is complete you will have to look into buildprot.F to see what is available.
      • nunit (integer)
      • The number of monomers in this molecule. Must be less than or equal to NUMAX (see preproc.h) and there is also a check in the builder to make sure you do not exceed NUMAX with the number of atoms that all of your monomers require.
      nmaxcbmc (integer)
      • The nmaxcbmc variable determines the largest number of atoms that are regrown during a configurational-bias regrowth. Since we only know the number of amino acids at this stage, and not the number of atoms, the final value of nmaxcbmc is computed as the product of the final number of atoms in the molecule times the input value of nmaxcbmc divided by the input value of nunit.
      forcefield (character)
      • The forcefield that you want to use to build this molecule. I'm working on better documentation of which force fields are implemented, but until that is finished just take a look in ffnonbond.F
      protgeom (character)
      • linear: The polypeptide will be generated starting from the N-terminus and finishing at the C-terminus.
      • cyclic: The polypeptide is cyclic so the first amino acid is bonded to the final amino acid.

      The variables listed immediately below are listed as a group for each amino acid in the molecule. There is only one line of input per building block in the molecule.

      pepname (character), stereochem (character), bondpartner (integer)
      • pepname is a two letter code for the building blocks of the molecule. Peptides use a code where the first letter is the one letter code for each amino acid. The second character is generally the charge state of the side chain, but has some different meanings for histidine and cysteine. Until the documentation is in place you need to look in buildprot.F to find a complete list of valid pepnames.
      • stereochem is a single letter which determines the stereochemistry of the peptide. The valid options are l (L-amino acid), d (D-amino acid) and r (racemic).
      • bondpartner is the number of the amino acid which is bonded to this amino acid through the side chain. This is only used for cysteines which have a disulfide bridge (type cs), otherwise just set this value to 0. The bondpartner integers refer to the amino acids starting with the first amino acid listed in towhee_input as amino acid #1.
      This is the end of the section that is repeated for each atom for inpstyle=1

       

    • 2: Atom-based connectivity map, with the details of the force field parameters determined via the buildmolec and assemble routines. This is the easiest way to set up any molecule that is not a series of amino acids. You must choose a forcefield and then input the appropriate parameter names for that force field. I'm working on better documentation of the atom names used in Towhee, but until that is complete you have to look in ffnonbond.F The program will sort out all of the vibration types, bending angles, bending types, regular torsion angles, regular torsion types, angle-angle terms, angle-angle types, and improper torsion types that are implied by the bonding structure of the molecule. I have not automated the atom assignment for the improper torsions as some of the force fields do not have general rules (at least not rules I can decipher) for determining where the improper torsions belong.
      • nunit (integer)
      • The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX (see preproc.h).
      nmaxcbmc (integer)
      • The maximum number of atoms to regrow during a configurational-bias regrowth. Generally I set this to the same value as nunit, but occasionally a molecule is so large that almost none of the moves which regrow large portions are accepted. In this case I set nmaxcbmc to be around 1/2 of nunit so that only smaller regrowths are performed.
      forcefield (character)
      • The forcefield that you want to use to build this molecule. I'm working on better documentation of which force fields are implemented, but until that is finished just take a look in ffnonbond.F

      The variables listed immediately below (unit through improper) are listed as a group for each atom in the molecule. Thus, you input all of the information about the first atom before you list information for the subsequent atoms.

      unit (integer), type (character), qqatom (double precision)
      • unit is the number of the atom in order starting from atom number 1. This is only used to help the user keep track of the molecule as they are building it in the input file. If the unit number listed in towhee_input does not match the running total of unit numbers in Towhee then the code will stop with an error message.
      • ntype is the character string that contains the atom type for the forcefield. I'm working on better documentation for the available atom types, but until that is ready you will need to look in ffnonbond.F. I generally use the same atom types as the original authors of the force field, but sometimes I have to add information to those atom types in order to automate the assembly process.
      • qqatom is the charge on this atom. This value is not used (but must still be input) if lcoulomb is false.
      vibration
        invib (integer)
        • The first line under the vibration heading is the number of atoms that are bonded to the current atom. Must be a number between 0 and NNBOND (see preproc.h).
        ijvib (integer)
        • The second line contains the atom numbers for all invib atoms that are bonded to the current atom.
      improper torsion
        inimprop (integer)
        • The first line under the improper heading is the number of improper torsions (any form) which have the central atom located at the current atom. You must list all improper torsions which have the current atom at the central position, but you do not list improper torsions which contain the current atom at one of the ends. Must be a number between 0 and ((NNBOND-1)*(NNBOND-2))/2 (see preproc.h).
        ijimprop2 (integer), ijimprop3(integer), ijimprop4 (integer), itimprop (integer)
        • The next inimprop lines underneath the improper torsion heading are a list of the other atoms in the improper torsion and the improper force field number (see ffimproper.F) for the inimprop improper torsions that contain the current atom at the central atom. There are currently three different forms of improper torsions, and these forms are specified in the force field (either in ffimproper.F or in towhee_ff). In all cases, the three atoms must all be bound to the current atom. If you want the program to determine the improper torsion type then just enter an itimprop value of 0.
          • Form 1: Amber / Stereo Improper. This type of improper torsion works by computing the dihedral angle between the planes formed by the atoms ijimprop2-current-ijimprop3 and ijimprop2-current-ijimprop4. This was originally used as a means to enforce planarity, but is also useful for enforcing stereochemistry. The format for the stereo improper torsion is to list atoms ijimprop2, ijimprop3, and ijimprop4 and the torsion type (itimprop) on each line, where there is one improper torsion per line of towhee_input.
          • Form 2: Charmm / Simple Out-of-Plane. The format for listing the simple out-of-plane improper torsion is to consider the current atom in the first position of a dihedral between atoms current-ijimprop2-ijimprop3-ijimprop4 so you only need to list atoms ijimprop2, ijimprop3, and ijimprop4 and the torsion type on each line, where there is one improper torsion per line of towhee_input.
          • Form 3: Averaged Out-of-Plane. The format for listing the averaged out-of-plane improper torsion is identical to the simple out-of-plane. The only difference is that the dihedral used is not just the current-ijimprop2-ijimprop3-ijimprop4, but is instead an average of the following three angles: current-ijimprop2-ijimprop3-ijimprop4; current-ijimprop3-ijimprop4-ijimprop2; current-ijimprop4-ijimprop2-ijimprop3.
      This is the end of the section that is repeated for each atom for inpstyle=2
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Last updated: September 15, 2004