Data

Tools

Indexes

Applications

Experiments

Awesome

An open API service indexing awesome lists of open source software.

https://github.com/paduagroup/fftool

Tool to build force field input files for molecular simulation
https://github.com/paduagroup/fftool

force-field lammps molecular-dynamics packmol

Last synced: 3 months ago
JSON representation

Tool to build force field input files for molecular simulation

Awesome Lists containing this project

README 

          
# fftool



[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.18618.svg)](http://dx.doi.org/10.5281/zenodo.18618)



_[Agilio Padua](http://perso.ens-lyon.fr/agilio.padua)_



This is a Python tool to build force field input files for molecular dynamics

simulations of systems composed of molecules, ions or extended materials.



`fftool` creates initial files for classical, fixed-charge molecular dynamics

simulations. A force field database ionic liquids is available in

[CL&P](https://github.com/agiliopadua/clandp). For polarizable force field and

simulations, check the [CL&Pol](https://github.com/agiliopadua/clandpol) tools

and database.



## Contents



* `fftool`: builds a simulation box and the corresponding force field for

    systems containing molecules, ions or extended materials. It requires the

    [Packmol](http://www.ime.unicamp.br/~martinez/packmol/) software to generate

    coordinates in the box. It outputs files in formats suitable for the

    [LAMMPS](http://lammps.sandia.gov/), [OpenMM](http://openmm.org),

    [GROMACS](http://www.gromacs.org) or

    [DL_POLY](http://www.stfc.ac.uk/CSE/randd/ccg/software/DL_POLY/25526.aspx)

    molecular dynamics packages.



* `tools/`: utility scripts.



* `examples/`: examples of molecule files and force field databases.



## Requirements



* [Python](http://www.python.org/)



* [Packmol](http://www.ime.unicamp.br/~martinez/packmol/) to pack

  molecules and materials in the simultion box.

  



## Obtaining



Download the files or clone the repository:



    git clone https://github.com/agiliopadua/fftool.git



## Tutorial



These are instructions on how to build an force field files and an initial

configuration for a system composed of molecules, ions or materials. 



1. For each molecule, ion or fragment of a material prepare a file with atomic

   coordinates and eventually connectivity (covalent bonds). The formats

   accepted by this tool are `.zmat`, `.xyz`, `.pdb` or `.mol`, which are

   common formats in computational chemistry.



   A `.zmat` file has the molecule name in the first line, followed by one empty

   line, then the z-matrix. See the `examples` directory and the Wikipedia entry

   [Z-matrix(chemistry)](https://en.wikipedia.org/wiki/Z-matrix).  Variables can

   be used in place of distances, angles and dihedrals. `fftool` infers

   connectivity (topology) from the z-matrix by default. In this case cyclic

   molecules require additional `connect` records to close rings. Improper

   dihedrals can be indicated by `improper` records. If a `reconnect` record is

   present, then connectivity will be guessed based on bond distances from the

   force field (see below). Below the z-matrix and the informations above, the

   name of a file with force field parameters can be supplied.



   The XYZ file format `.xyz` contains atomic coordinates only. The name of a

   file with force field parameters can be given in the second line after the

   molecule name, and in this case connectivity is deduced from the bond lengths

   in the force field.



   The PDB file format `.pdb` is widely used for proteins. The name of a file

   with force field parameters can be given on a `COMPND` record after the

   molecule name.  `fftool` infers connectivity from the bond lengths in the

   force field (`CONECT` records are not read).

 

   The MDL Molfile `.mol` file format contains a table with coordinates and

   also bonds. The name of a file with force field parameters can be given in

   the first line after the molecule name or in the third line. If the keyword

   `reconnect` is present after the force field filename, then connectivity

   will be deduced based on bond distances from the force field.



   There are many tools ([Open Babel](http://openbabel.org/),

   [Avogadro](http://avogadro.cc/), [VESTA](http://jp-minerals.org/vesta/en/))

   to create file in the above formats. Manual editing of the files is usually

   necessary in order to match the atom names with those of the force field.



2. Use `fftool` to create an input file for `packmol`, which will use new

   `_pack.xyz` files with atomic coordinates for the components of your

   system. For help type `fftool -h`. For example, to build a simulation box

   with 40 ethanol and 300 water molecules and a density of 38.0 mol/L do:



        fftool 40 ethanol.zmat 300 spce.zmat -r 38.0



    Alternatively, the side length of the the simulation box (here cubic) can

    be supplied in angstroms:



        fftool 40 ethanol.zmat 300 spce.zmat -b 20.0



3. Use `packmol` with the `pack.inp` file just created to generate the

   atomic coordinates in the simulation box:



        packmol < pack.inp



   A difficult convergence may indicate that density is too high, so adjust

   density or box size if necessary. For more complex spatial arrangements of

   molecules and materials you can modify the `pack.inp` to suit your needs (see

   the [Packmol](http://www.ime.unicamp.br/~martinez/packmol/) documentation).

   Atomic coordinates for the full system are written to `simbox.xyz`.



4. Use `fftool` to create input files for LAMMPS (-l), OpenMM (-x), GROMACS

   (-g) ou DL_POLY (-d) containing the force field parameters and the

   coordinates of all the atoms (taken from `simbox.xyz`):



        fftool 40 ethanol.zmat 300 spce.zmat -r 38.0 -l



    If no force field information was given explicitly in the molecule files, a

    default LJ potential with parameters zeroed will be assigned to atoms. No

    terms for bonds, angles or torsions will be created. This is suitable when

    working with non-additive, bond-order or other potentials often used for

    materials. The input files for MD simulations will have to be edited

    manually to include interaction potentials.



## Deducing Bonds and Angles



When inferring connectivity from atomic coordinates, distances in the

coordinates file are compared with equilibrium distances specified for bonds in

the force field, and a tolerance of +/-0.25 angstrom is used to decide if a bond

is created. So, the bond lengths in the conformation present in the molecule

file must be close to those in the force field specification for those bonds to

be included in the potential energy fonction of the system. The user is advised

to check the number of bonds by creating a test system with the minimum of

molecules.



Angles will be assigned to groups of three atoms i-j-k, with i-j and j-k bonded,

if the value of the angle in the conformation from the molecule file is within

+/-15 degrees of the equilibrium angle in the force field. If not, even if the

atoms i-j-k are bonded, their angle will not be present in the final potential

energy function, although topologically the angle is there. When running

`fftool` to create a force field file (with `-l`, `-x`, ` -g` or `-d` option) a

warning message will show which such topological angles have been "removed"

because they deviate too much from the equilibrium angles in the force

field. This removal of angles avoids problems with atoms that have more than

four ligands, such as S or P atoms with five or six ligands. Around these

centers there are topological angles of 180 degrees to which no potential energy

of bending is attributed in force fields. For example, in the octahedral PF6-

anion there are two different values of F-P-F angles: twelve 90 degree angles

between adjacent F atoms, and three 180 degree angles between opposite F atoms;

only the twelve 90 degree angles contribute with a harmonic potential energy

function in most force fields.



The tolerances for bond distances and angle values, 0.25 angstrom and 15

degrees, respectively, were chosen based on judgement. They can be set by

editing the `fftool` source, namely the global variables `BondTol` and

`AngleTol`. Use with care because spurious bonds and angles may be created if

the tolerances are set too large.



## Improper Dihedrals



Improper dihedrals are often used to increase the rigidity of planar atoms (sp2)

and differ from proper dihedrals in how they are defined. A proper dihedral

i-j-k-l is defined between bonded atoms i-j, j-k, and k-l and corresponds to

torsion around bond j-k, the dihedral being the angle between planes i-j-k and

j-k-l. An improper dihedral i-j-k-l is defined between bonded atoms i-k, j-k and

k-l, therefore k is a central atom bonded to the other three. `fftool` assumes

the central atom of the improper dihedral to be the third in the list. Often in

force fields the same potential energy function is used both for proper and

improper torsions.



If `improper` records are supplied in a molecule file (in `.zmat` format) then

those improper dihedrals are read by `fftool`. Otherwise, the script will search

for candidate improper dihedrals on all atoms with three bonds, whatever the

input format. Warning messages will be printed if there are atoms with three

bonds, and these messages can be ignored if the atoms in question are not

centers of improper torsions. The user is advised to check the number and order

of the atoms in the true improper dihedrals in the files created, by testing

with a minimal system.



## Periodic Boundary Conditions



In molecular systems the initial configuration will generaly not contain

molecules crossing boundaries of the simulation box. A buffer distance of 1.5

angstrom is reserved at the box boundaries to avoid overlap of molecules from

periodic images in the initial configuration, as explained in the `packmol`

documentation (this empty space is added by `fftool` only for orthogonal

boxes). So the user should be aware of this empty volume when choosing the size

of the box.



For simulations with extended materials it is possible to create chemical bonds

across boundaries. Option `-p` allows specification of periodic conditions along

x, y, z or combinations thereof. It is important in this case to supply box

dimensions using the option `-b ` for a cubic box, `-b ` for a

general orthogonal box, or `-b ` for a general

parallelepiped (triclinic box). An energy minimization step prior to the start

of the MD simulation is highly recommended because `fftool` will leave no extra

space near the boundaries and certain molecules may overlap with those of

neighboring images.



The coordinates of the atoms of the material have to be supplied in `.xyz`

format and prepared carefully so that distances across periodic boundaries are

within the tolerance to identify bonds. The user is advised to check the number

of bonds in the output files created.



It is important that only the material for which bonds are to be established

across boudaries is supplied in `.xyz` format. The initial files for other

molecules in the system should be in `.zmat` or `.mol` formats, which contain

connectivity information. This is to avoid spurious bonds between atoms of the

molecular species that may happen to be positioned too close to boundaries.



The `pack.inp` file will likely need manual editing in order to position the

atoms of the material precisely.



## Force Field File Format



The `fftool` script reads a database of molecular force field parameters in `xml` format (similar to the format used by OpenMM), or in the original `.ff` format described below. See the `examples` directory.



The `ff2xml` script converts from the original to the `xml` format.



### .ff format



Blank lines and lines starting with `#` are ignored.



There are five sections, with headings `ATOMS`, `BONDS`, `ANGLES`, `DIHEDRALS`

and `IMPROPER`. Under each section heading, registers concerning the different

types of term in the force field are given.



`ATOMS` records describe, for each type of atom:

* the non-bonded atom type used for intermolecular interactions (these

  types may differ in the charges or intermolecular potential

  parameters)

* the bonded atom type used in intermolecular interactions (these

  types determine the intramolecular terms such as bonds, angles

  dihedrals)

* the mass in atomic units

* the electrostatic charge in elementary units

* the non-bonded potential type, e.g. `lj`

* potential parameters, namely Lennard-Jones `sigma` (angstrom) and `epsilon`

  (kJ mol-1)



        C3H   CT  12.011  -0.18   lj    3.50   0.27614



`BONDS` records describe covalent bonds between intramolecular atom types:

* two bonded atom types

* type of bond potential, e.g. `harm` for harmonic potential or

  `cons` for a constrained bond.

* bond potential parameters, namely equilibrium distance (angstrom) and force

  constant in the form k/2 (x - x0)^2 (kJ mol-1 A-2)



        CT  CT   harm   1.529   2242.6



`ANGLES` records describe valence angles between intramolecular atom types:

* three bonded atom types, in which the central atom is bonded to the other

  two, e.g. i-j and j-k are bonded.

* type of angle potential, e.g. `harm` for harmonic potential or

  `cons` for a constrained angle.

* angle potential parameters, namely equilibrium angle (degrees) and force

  constant in the form k/2 (x - x0)^2 (kJ mol-1 rad-2)



        HC  CT  CT   harm   110.7   313.8



`DIHEDRALS` records describe torsion angles between intramolecular

atom types:

* four bonded atom types, in which atoms i-j, j-k, k-l are bonded.

* type of dihedral potential, e.g. `opls` for OPLS cosine series with

  four terms.

* dihedral potential parameters, with the coefficients in the form V_n/2

  (1 +/- cos(n phi)) (kJ mol-1).



        CT  CT  CT  CT   opls    5.4392   -0.2092    0.8368    0.0000



`IMPROPER` records describe improper dihedral angles between

intramolecular atom types:

* four bonded atom types, in which atoms i-k, j-k, k-l are bonded.

* type of dihedral potential, e.g. `opls` for OPLS cosine series with

  four terms.

* dihedral potential parameters, with the coefficients in the form

  V_n/2 (1 +/- cos(n phi)) (kJ mol-1).



        CA  CA  CA  HA   opls    0.0000    9.2048    0.0000    0.0000



## References



* [Packmol](http://www.ime.unicamp.br/~martinez/packmol/):

  L. Martinez et al. J Comp Chem 30 (2009) 2157, DOI:

  [10.1002/jcc.21224](http://dx.doi.org/10.1002/jcc.21224) 

  

* [LAMMPS](http://lammps.sandia.gov/): S. Plimton, J Comp Phys

  117 (1995) 1, DOI:

  [10.1006/jcph.1995.1039](http://dx.doi.org/10.1006/jcph.1995.1039)



* [OpenMM](http://openmm.org): P. Eastman, J. Swails, J. D. Chodera,

  R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett,

  M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, and

  V. S. Pande. PLOS Comp. Biol. 13 (2017) e1005659, DOI:

  [10.1371/journal.pcbi.1005659](https://doi.org/10.1371/journal.pcbi.1005659)



* [GROMACS](http://www.gromacs.org/): H.J.C. Berendsen, D. van der

  Spoel, R. van Drunen, Comp Phys Commun, 91 (1995) 43, DOI:

  [10.1016/0010-4655(95)00042-E](https://doi.org/10.1016/0010-4655(95)00042-E)



* [DL_POLY](http://www.stfc.ac.uk/CSE/randd/ccg/software/DL_POLY/25526.aspx):

  I.T. Todorov and W. Smith, Daresbury Lab.