SourceForge.net Logo
MCCCS Towhee (towhee_input Version 4.3.x)

 

 

 Overview
    This section covers the variables that are set in the towhee_input file Version 4.3.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.

    Note that for each variable listed below you must include the name of the variable on the previous line. In addition, the variables that are subsets of various Monte Carlo moves must be indented 10 spaces.
Bug reports / feature enhancements for 4.3.x versions
  • 4.3.3: Added the DREIDING force field and some related new intramolecar potential forms. Added examples for DREIDING and UFF.
  • 4.3.2: Added the Universal Force Field (UFF) along with a handful of new functional forms required for this force field. Fixed a slight bug that was reporting the running block averages of the number density off by a factor of 1000 (the final results were correct, just the values during the run were incorrect).
  • 4.3.1: Added the Gordon n-6 potential along with a token example forcefield.
  • 4.3.0: Removed the integer variables potentype and mixrule and replaced them with the similar character string variables classical_potential and classical_mixrule. Added a few angle terms to OPLS-2001 and fixed up some of the naming conventions for the dihedral terms as well. Introduced a new force field version number, but the code is still compatible with the previous version.
towhee_input file differences from version 4.2.x
  • replaced the integer variable potentype with the character string variable classical_potential
  • replaced the integer variable mixrule with the character string variable classical_mixrule
  • variables associated with the cbstyle variables are now only listed if they are needed. This affects all of the sdev*** variables and the vibrang
Variable explanations for towhee_input
    randomseed (integer)
    • The 32 bit integer seed that is used to initialize the ranlux random number generator. Must be positive.
    inputformat (character string)
    • 'Towhee' : reads in the input variables following the format for Towhee. This format 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.
    • 'Database' : reads in the input variables from the database_input file. Runs energy calculations for a database of conformations. See the towhee_input database format for more information about this feature.
    ensemble (character string of size 3)
    • 'npt': Isobaric-Isothermal Ensemble. The volume moves for each simulation box are performed in an exchange with an external pressure bath set at a specified pressure. The total number of molecules is conserved.
    • 'nvt': Canonical Ensemble. The total volume of the system is conserved. The total number of molecules in the system is conserved. In the case of a multi-box simulation this exchanges volume between pairs of boxes (canonical Gibbs ensemble).
    • 'uvt': Grand Canonical Ensemble. The total volume of the system is conserved. The total number of molecules in the system equilibrates with an external ideal gas bath set at a specified chemical potential.
    temperature (double precision)
    • The temperature in Kelvin.
    The variable in this subsection is only included in the input file if ensemble is set to 'npt'
    pressure (double precision)
    • The external pressure in kPa.
    End of the subsection only included if ensemble is 'npt'
    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) [one value for each molecule type]
    • The number of molecules of each type (listed sequentially on a single line). For the constant N ensembles (nvt, npt) this is the actual number of molecules in the simulation. For the constant chemical potential ensembles (uvt) this is the maximum number of molecules allowed in the simulation.
    The variable in this subsection is only included in the input file if ensemble is set to 'uvt'
    chempot (double precision)
    • The real chemical potential (this includes intramolecular portions and is identical to the CB chemical potential output by the code) for molecules of each type (listed sequentially on a single line). The units are in Kelvin divided by Boltzmann's constant (identical to the output CB chemical potential).
    End of the subsection only included if ensemble is 'uvt'
    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) and some Monte Carlo moves are only valid for multiple box ensembles.
    stepstyle (character string of length 10)
      The different settings for stepstyle require a different set of variables afterwards. For each stepstyle I list a description of the resutling step style and the set of variables that must follow.
    • 'cycles': Run a Monte Carlo simulation for nstep Monte Carlo cycles. A cycle is equal to N Monte Carlo moves, where N is the number of molecules in the system.
        • nstep (integer)
        • The number of Monte Carlo steps to perform where each step is a cycle.
    • 'moves': Run a Monte Carlo simulation for nstep Monte Carlo moves.
        • nstep (integer)
        • The number of Monte Carlo steps to perform where each step is a single move.
    • 'minimize': Perform a minimization.
        • optstyle (integer)
        • 1: Use the Broyden-Fletcher-Goldfarb-Shanno variant of the variable-metric or quasi-newton method for minimization. The suggested reference in Numerical Recipes was Polak 1971.
        mintol (double precision)
        • The convergance tolerance for the minimization.
    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.
    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.
    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.
    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.
    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.
    The variables in this subsection are only included if ensemble is 'uvt'
    louthist (logical)
    • .true. if you wish to output files used for histogram reweighting. When set to this value you must also include two additional variables
      • histcalcfreq (integer)
      • The step frequency for computing the information needed for histogram reweighting.
      histdumpfreq (integer)
      • The step frequency for outputting the information needed for histogram reweighting to the various towhee_histogram files. The ratio of histdumpfreq/histcalcfreq must be less than the NDUMPHIST value specified in preproc.h.
    • .false. if you do not wish to output files for histogram reweighting. No additional variables are required for this setting.
    End of the subsection only included if ensemble is 'uvt'
    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.
    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.
    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.
    chempotperstep (integer)
    • The number of additional trial insertions to perform in each box for at the end of every Monte Carlo step (listed sequentially for each molecule type on a single line). This allows the measurement of chemical potential in ensembles that do not have an insertion and deletion move (such as canonical and isobaric-isothermal).
    potentialstyle
    • 'classical': uses a classical intermolecular potential to describe the energies between atoms. This is currently the only fully functional option for potentialstyle, although some quantum options are under active development and should be available soon.
    The variables in this subsection are only included in the input file if potentialstyle is set to 'classical' or 'quantum//classical'
    ffnumber (integer)
    • 1 or more: reads the force field information from this number of file(s) listed in the ff_filename.
    ff_filename (formatted character*70) [one line for each force field]
    • A list of the filenames (one per line) that contain the force field information.
    classical_potential (character*30)
      The setting for this variable controls the nonbonded potential type. Depending on the setting there are a number of other variables that are also required. Please see the classical_potential web page for more information.
    coulombstyle (character*20)
    • 'none' if you do no want to compute any coulombic interactions.
    • 'ewald_fixed_kmax' if you want to use point charges with an Ewald sum that utlilizes a constant number of inverse space vectors (kmax) and a variable electrostatic cutoff (rcelect) equal to half the current box length. When using this option you will also need to list the following variables.
        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.
    • 'ewald_fixed_cutoff' if you want to use point charges with an Ewald sum that utilizes a constant electrostatic cutoff (rcelect) and adjusts the number of inverse space vectors (kmax) according to the following heuristic.
      alpha = ( 1.35 - 0.15 log[ewald_prec]) / rcelect
      kmax = ( alpha * Max[box length] / Pi) * (log[ewald_prec])0.5
      When using this option you will also need to list the following variables.
        ewald_prec (double precision)
        • Controls the precision of the Ewald summation technique. The smaller the value, the better the results (and the more expensive the simulation). The recommended value of 1d-4 is generally adequate, while a value of 1d-5 is very good (but more expensive).
        rcelect (double precision)
        • The cutoff for electrostatic interations computed in the "real space" portion of the Ewald sum. Decreasing this value means less work in the "real space", but correspondingly more work in the "inverse space". Setting this equal to the general nonbonded cutoff (see rcut in potentype) is recommended.
        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.
    nfield (integer)
      The number of external fields to apply in the simulation. These fields can take on a variety of forms, but are always applied relative to a plane in one of the simulation boxes. Typical uses are for simulating the effect of a rigid surface without having to treat the surface atoms explicitly. If nfield is set to anything other than 0 you will need to list the following variables for each field you wish to specify.
      fieldtype (character*20)
      • 'Hard Wall': Places a hard wall of a specified diameter in one of the boxes. This wall excludes the center of each atom in the simulation, so a hard wall with a radius of 6.0 would exclude all atoms within 6.0 Angstroms of its center point. With this option you must also specify the following variables.
          hrdbox (integer)
          • This is the number of the simulation box which contains this hard wall. Must range from 1 to numboxes.
          hrdxyz (character*1)
          • 'x': hard wall is perpendicular to the x-axis (in the yz plane)
          • 'y': hard wall is perpendicular to the y-axis (in the xz plane)
          • 'z': 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 potentype or any of the atom parameters. The wall is felt through the periodic boundaries.
      • 'Hooper Umbrella': Places a Hooper Umbrella field (see Hooper et al. 2000) in a simulation box. This is a 4th power energy function based on displacement along a single axis.
        v(d) = umba * [ (d - umbcenter) / umbcenter ]
        With this option you must also specify the following variables.
          umbbox (integer)
          • This is the number of the simulation box which contains this Umbrella field. Must range from 1 to numboxes.
          umbxyz (character*1)
          • 'x': Field is perpendicular to the x-axis (in the yz plane)
          • 'y': Field is perpendicular to the y-axis (in the xz plane)
          • 'z': Field is perpendicular to the z-axis (in the xy plane)
          umbcenter (double precision)
          • The zero energy point of the field, listed as a distance in Angstroms along the axis specified in umbxyz
          umba (double precision)
          • The energy constant in units of K/kB.
      • 'LJ 9-3 Wall': Places a 9-3 Lennard-Jones wall in one of the simulation boxes The wall potential has the following functional form.
        v(d) = [ 2/3 Pi Epswf sigwf3 rhowall ] * [ 2/15 (sigwf/d)9 - (sigwf/d)3 ]
        With this option you must also specify the following variables.
          ljfbox (integer)
          • This is the number of the simulation box which contains this Lennard-Jones wall. Must range from 1 to numboxes.
          ljfxyz (character*1)
          • 'x': Lennard-Jones wall is perpendicular to the x-axis (in the yz plane)
          • 'y': Lennard-Jones wall is perpendicular to the y-axis (in the xz plane)
          • 'z': 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.
          ljfdir (integer)
          • -1: Atoms only interact with the "left" face of this wall. Unlike the hard walls, this does not extend through the periodic boundary.
          • 1: Atoms only interact with the "right" face of this wall. Unlike the hard walls, this does not extend through the periodic boundary.
          ljfcut (double precision)
          • The distance beyond which the wall-atom interactions are not computed and assumed to be zero.
          ljfshift (logical)
          • T: if you want to shift the lj wall potential to be zero at the cutoff.
          • F: if you do not want to shift the potential.
          ljfrho (double precision)
          • The number density of atoms in the integrated wall potential (units of atoms per cubic Angstrom).
          ljfntypes (integer)
          • The number of atom types in the system that interact with the wall. Any atom type not listed here will have zero interaction with the wall. For each value of you must list the following variables.
              ljfname (character*6)
              • The name of the atom. This must match up with the atom names listed down in the inpstyle 2 portion of each molecule that is interacting with this wall. If you are not using that inpstyle this will still work except you will need to know the atom names in the appropriate towhee_ff_whatever files.
              ljfsig (double precision)
              • Sigma parameter for the interaction between this atom and the wall atoms. Units are Angstroms.
              ljfeps (double precision)
              • Epsilon parameter for the interaction bewteen this atom and the wall atoms. Units are K/kB.
      • 'Steele Wall': Places a 10-4 Lennard-Jones wall in one of the simulation boxes The wall potential has the following functional form.
        v(z) = epsilonw [ 2/5 (sigmasf/z)10 - (sigmasf/z)4 - sigmasf4 / [ 3 Delta ( z + 0.61 Delta )3 ] ]
        where
        epsilonw = 2 Pi epsilonsf rhos sigmasf2 Delta
        This potential is attributed to Steele 1973, but I found that reference a bit confusing so I implemented the equations as presented in Lastoskie et al. 1993 and the variable names here follow the notation in that paper.
        With this option you must also specify the following variables.
          steele box (integer)
          • This is the number of the simulation box which contains this Steele wall. Must range from 1 to numboxes.
          steele xyz (character*1)
          • 'x': wall is perpendicular to the x-axis (in the yz plane)
          • 'y': wall is perpendicular to the y-axis (in the xz plane)
          • 'z': wall is perpendicular to the z-axis (in the xy plane)
          steele surface (double precision)
          • Position of the surface of the wall. Must be between 0.0 and the box length of the axis that is perpendicular to the wall.
          steele dir (integer)
          • -1: Atoms only interact with the "left/bottom" face of this wall. Unlike the hard walls, this does not extend through the periodic boundary.
          • 1: Atoms only interact with the "right/top" face of this wall. Unlike the hard walls, this does not extend through the periodic boundary.
          steele cutoff (double precision)
          • The distance beyond which the wall-atom interactions are not computed and assumed to be zero.
          steele shift (logical)
          • T: if you want to shift the wall potential to be zero at the cutoff.
          • F: if you do not want to shift the potential.
          steele delta (double precision)
          • The spacing between the layers in the solid represented by this surface potential. Units are in Angstroms.
          steele rho_s (double precision)
          • The density of the atom in the solid represented by this surface potential. Units are in atoms per cubic Angstrom.
          steele ntype (integer)
          • The number of atom types in the system that interact with the wall. Any atom type not listed here will have zero interaction with the wall. For each type you must list the following variables.
              steele name (character*6)
              • The name of the atom. This must match up with the atom names listed down in the inpstyle 2 portion of each molecule that is interacting with this wall. If you are not using that inpstyle this will still work except you will need to know the atom names in the appropriate towhee_ff_whatever files.
              sigma_sf (double precision)
              • Sigma parameter for the interaction between this atom and the wall atoms. Units are Angstroms.
              epsilon_sf (double precision)
              • Epsilon parameter for the interaction bewteen this atom and the wall atoms. Units are K/kB.
    isolvtype (integer)
    • 0: Perform a simulation without any implicit solvation. This is the default choice for performing a simulation.
    • 1: not yet working.
    • 2: solvation using the Charmm19-EEF1 potential.
    • 3: solvation using the classical density functional theory code Tramonto to compute a solvation free energy. The Tramonto code is not yet publically available.
    End of the subsection that is only included in the input file if potentialstyle is set to 'classical' or 'quantum//classical'
    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 and on each line one value for each molecule type]
      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.
    • 3: The coordinates for each atom are read from towhee_nanotube. This file is generated by the Towhee code if you use the inpstyle for carbon nanotubes.
    • 4: The molecule is generated by placing some of the backbone atoms onto a helix and then growing the rest of the atoms using CBMC. Any molecule initialized using this style must have the following information listed subsequent to the initstyle variables.
        helix_moltyp (integer)
          An integer corresponding to the molecule type that had an initstyle variable set to 4 in one of the simulation boxes. These must be listed in consecutive order.
        helix_radius (double precicion)
          The radius of the helix (units of Angstroms).
        helix_angle (double precision)
          The pitch angle the helix makes with respect to the z-axis (units of degrees).
        helix_keytype (character*10)
        • 'element' compares the helix_keyname with the character*2 variable element that contains the 2 letter elemental code for each atom.
        • 'nbname' compares the helix_keyname with the character*10 variable nbname that contains the 10 character code for each atom type. This is the same variable that is used when inputting the atom names with the Atom-based connectivity map (inpstyle 2).
        • 'pdbname' compares the helix_keyname with the character*4 variable pdbname that contains the 4 character code used in the pdb format output. This is most suitable for use with the Polypeptide builder (inpstyle 1) or the Nucleic acid builder (inpstyle 4).
        helix_keyname (character*10)
          The key for finding matches of the atom with the data structures for the molecule that is being grown as a helix. You need to choose an atom name that only appears in the backbone (e.g. 'P' for Charmm27 nucleic acids when using the element keytype, or ' CA ' for the C alpha backbone carbon of a polypeptide when using the pdbname keytype).
        helix_conlen (double precision)
          The distance between consecutive helix_element atoms (units of Angstroms).
        helix_phase (double precision)
          The initial angle of the helixcal chain (units of degrees). Normally, this has little effect as it is just a rotation about the z-axis, but if you are trying to set up two complementary nucleic acid chains to form a double helix then you would want their phase angles to differ by 180 degrees.
    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 in 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.
  • 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.
  • Comment: The formatting of the move variables is now very specific. In all cases the first variable for a move (pm***) is left justified (as is the standard for most variable) while all other variables for that move are indented 10 spaces.
    • Isotropic Volume Move: These variables are only included for the following cases
    • ensemble is 'npt'
    • ensemble is 'nvt' and numboxes is 2 or more.
    pmvol (double precision)
    • Probability of performing a volume move. If (ensemble is 'npt') then a single box is selected and it exchanges volume with an external pressure bath (see pressure). If (ensemble = 'nvt' 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 (ensemble = 'npt') then a value of pmvlpr is listed for each box. If (ensemble = 'nvt') 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) [a single value regardless of the actual number of box pairs]
      • The initial volume maximum displacement. If this is an isobaric-isothermal ensemble (ensemble = 'npt') then this is the initial maximum volume displacement (cubic Angstroms) in each box. If this is the canonical Gibbs ensemble (ensemble = 'nvt' 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.
    Anisotropic Volume Move: These variables are only included for the following cases
    • ensemble is 'npt'
    • ensemble is 'nvt' and numboxes is 2 or more.
    pmcell (double precision)
    • Probability of performing a unit cell adjustment move. If (ensemble = 'npt' ) 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 (ensemble = 'nvt' 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 (ensemble = 'npt') then a value of pmvlpr is listed for each box. If (ensemble = 'nvt') 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 (ensemble = 'nvt'). 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.
    Rotational-bias 2 box molecule Transfer Move: These variables are only included if numboxes is greater than or equal to 2
    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 nch_nb_one 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).
    Configurational-bias 2 box molecule Transfer Move: These variables are only included if numboxes is greater than or equal to 2
    pm2boxcbswap (double precision)
      pm2cbswmt (double precision)
      • Probability of performing a configurational-bias interbox molecule transfer move on each type of molecule in the system.
      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).
    Configurational-bias grand-canonical insertion/deletion Move: These variables are only included if ensemble is 'uvt'
    pmuvtcbswap (double precision)
    • Probability of performing a grand-canonical configurational-bias insertion or deletion move.
      pmuvtcbmt (double precision)
      • Probability of performing a grand-canonical configurational-bias insertion or deletion move on each type of molecule in the system.
    Configurational-bias single box molecule Reinsertion Move
    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.
      pm1cbswmt (double precision)
      • Probability of performing an intrabox configurational-bias molecule transfer move on each type of molecule in the system.
    Aggregation Volume Bias Move Type 1
    pmavb1 (double precision)
    • Probability of performing an aggregation volume bias move of type 1, as described in Chen and Siepmann 2000. This is useful for forming and destroying clusters in simulations with molecules that tend to aggregate together.
      pmavb1in (double precision)
      • Probability of trying to move a molecule into an inner region for aggregation volume bias move of type 1.
      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.
    Aggregation Volume Bias Move Type 2
    pmavb2 (double precision)
    • Probability of performing an aggregation volume bias move of type 2, as described in Chen and Siepmann 2001. This is useful for forming and destroying clusters in simulations with molecules that tend to aggregate together.
      pmavb2in (double precision)
      • Probability of trying to move a molecule into an inner region for aggregation volume bias move of type 2.
      pmavb2mt (double precision)
      • Probability of performing an aggregation volume bias move of type 2 where a molecule of a certain type is moved. This is an array with one element for each molecule type.
      pmavb2ct (double precision)
      • Probability of performing an aggregation volume bias move of type 2 where the molecule target is of a certain type. The molecule that is moved is chosen according to pmavb2mt 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.
      avb2rad (double precision)
      • The radius used to define the inner and outer volumes in the aggregation volume bias move of type 2. The distance is specified in Angstroms and must be greater than zero, but less than or equal to rcut.
    Aggregation Volume Bias Move Type 3
    pmavb3 (double precision)
    • Probability of performing an aggregation volume bias move of type 3, as described in Chen and Siepmann 2001. This is useful for transfering molecules between clusters.
      pmavb3mt (double precision)
      • Probability of performing an aggregation volume bias move of type 3 where a molecule of a certain type is moved. This is an array with one element for each molecule type.
      pmavb3ct (double precision)
      • Probability of performing an aggregation volume bias move of type 3 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.
      avb3rad (double precision)
      • The radius used to define the inner and outer volumes in the aggregation volume bias move of type 3. The distance is specified in Angstroms and must be greater than zero, but less than or equal to rcut.
    Configurational-Bias Partial Molecule Regrowth
    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.
    Configurational-Bias Protein backbone Regrowth
    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.
    Torsional Pivot Move
    pmpivot (double precision)
    • Probability of performing a pivot move about a random bond in the molecule. This move chooses a bond that is not part of a cyclic geometry, and has at least one bond emenating from each end, and then rotates one side of the molecule about that bond.
    Concerted Rotation Move on a non-peptide backbone
    pmconrot (double precision)
    • Probability of performing a concerted rotation move for a sequence of 9 atoms in a molecule.
    Concerted Rotation Move over a 3 peptides backbone sequence
    pmcrback (double precision)
    • Probability of performing a concerted rotation move on a sequence of three peptides in a polypeptide. This move only works for polypeptides.
      pmcrbmt (double precision)
      • Probability of performing a protein backbone concerted rotation move on each type of molecule in the system.
    Plane Shift Move
    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.
    Row Shift Move
    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.
    Intramolecular Single Atom Translation Move
    pmtraat (double precision)
    • Probability of performing a single-atom translation 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, selects a vector on a unit sphere 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 are updated to yield the desired acceptance rate for each molecule type in each box (see trmaxdispfreq).
      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 trmaxdispfreq) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    Center-of-Mass Molecule Translation Move
    pmtracm (double precision)
    • Probability of performing a center-of-mass translation 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, chooses a vector on a unit sphere 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 are updated to yield the desired acceptance rate for each molecule type in each box (see trmaxdispfreq).
      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 trmaxdispfreq) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    Rotation about the Center-of-Mass Move
    pmrotate (double precision)
    • Probability of performing a rotation about the center-of-mass move for a molecule without regard to the box the molecule is currently located in. This move chooses a molecule of the appropriate type at random and then attempts to rotate the entire molecule about the x, y, and z axes that run through the center-of-mass a random number of radians between -rmrot and +rmrot around each of the three axes.
      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 are updated to yeild the desired acceptance rate for each molecule type in each box (see trmaxdispfreq).
      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 trmaxdispfreq) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
    tor_cbstyle (integer)
    • 0: When performing a configurational-bias move, generate trial dihedral angles according to the true, ideal probability distribution. This is the method described in Martin and Siepmann 1999
    • 1: When performing a configurational-bias move, generate trial 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. When using this option you must also include the following variable.
        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 tor_cbstyle 1. Specify a value in degrees. Right now I am using a value of 20.0.
    bend_cbstyle (integer)
    • 0: When performing a configurational-bias move, generate trial bending angles according to the true, ideal probability distribution. This is the method described in Martin and Siepmann 1999
    • 1: When performing a configurational-bias move, generate trial bending 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. When using this option you must also include the following variables.
        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 bend_cbstyle 1. Specify a value in degrees. Right now I am using a value of 10.0.
        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 bend_cbstyle 1. Specify a value in degrees. Right now I am using a value of 20.0.
    vib_cbstyle (integer)
    • 0: When performing a configurational-bias move, generate trial bond lengths according to the true, ideal probability distribution within the ranges set by the vibrang variable. When using this option you also need to incude the following variable.
    • 1: When performing a configurational-bias move, generate trial bond lengths 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. When using this option you must also include the following variable.
        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 vib_cbstyle 1. Specify a value in Angtroms. Right now I am using a value of 0.1.
    cdform (integer)
    nch_nb_one (integer) [one value for each molecule type]
    • This is the number of trial positions that are sampled for the first atom inserted during a configurational-bias or rotational-bias molecule exchange move (see pm2boxrbswap, pm2boxcbswap, and pm1boxcbswap). I typically use a value of 10. The value must be less than or equal to NCHMAX (see preproc.h).
    nch_nb (integer) [one value for each molecule type]
    • 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 pm2boxcbswap and pm1boxcbswap). 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).
    nch_tor_out (integer) [one value for each molecule type]
    • This is the number of outer loops over the dihedral angles that are sampled during configurational-bias moves with cdform = 1. This has no meaning for cdform = 0. I typically use a value in the range 1 to 10 with cdform = 1. The value must be less than or equal to NCHTOR_MAX (see preproc.h).
    nch_tor_in (integer) [one value for each molecule type]
    • 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 for tor_cbstyle 0 and in the range 10 to 100 for tor_cbstyle 1. The value must be less than or equal to NCHTOR_MAX (see preproc.h).
    nch_tor_in_con (integer) [one value for each molecule type]
    • 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. 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).
    nch_bend_a (integer) [one value for each molecule type]
    • 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 bend_cbstyle of 0, and 10 for bend_cbstyle of 1.
    nch_bend_b (integer) [one value for each molecule type]
    • 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 bend_cbstyle of 0, and 10 for bend_cbstyle of 1.
    nch_vib (integer) [one value for each molecule type]
    • 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 vib_cbstyle 0 and 10 for vib_cbstyle 1, unless I am using a fixed-bond length force field, in which case you might as well just use 1.

     

    The final section of towhee_input contains the information that is used to construct the forcefield for the molecule types in the system. The choice of inpstyle determines which other variables are required to describe the molecule. Click on the appropriate link for each inpstyle to learn about the remaining variables that are required for each case.
    inpstyle (integer)
Return to the main towhee web page

 
Send comments to: Marcus G. Martin
Last updated: December 08, 2004