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use_fftool.md

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fftool

A python tool to create initial files for molecular dynamics simulatons

Yawei Liu

2021/11/30

before use

  • python and packmol are required.

  • pypy is recommened for large systems.

  • fftool needs two types of files for each species (molecules, ions and other materials) in MD simulations

    • a topology file with atomic coordinates and eventually connectivity (covalent bonds)
    • a force field file with parameters for the masses, the atomic charges, non-bond interactions and bond (including bond, angle, diheral and improper) interactions.
    • you can find some examples in example

  • alway test your files with a minimal system

  • More detailed information can be found here.

topology file

  • The formats accepted by fftool are .zmat, .xyz, .pdb or .mol.

  • Each file contains the filename for the force field.

  • fftool can deduce the connectivity between atoms based on the bond length in the force field file.

    • reconnect is always performed for .xyz and .pbd files.
    • reconnect is performed for .zmat and .mol files if a reconnect keyword is given.

  • .zmat file is always recommend, especially for building an own custom molecule.

    • this is an example for benzene
    benzene

CA
CA  1  rCC
CA  2  rCC  1  120.00
CA  3  rCC  2  120.00  1   0
CA  4  rCC  3  120.00  2   0
CA  5  rCC  4  120.00  3   0
HA  1  rCH  2  120.00  3 180
HA  2  rCH  3  120.00  4 180
HA  3  rCH  4  120.00  5 180
HA  4  rCH  5  120.00  6 180
HA  5  rCH  6  120.00  1 180
HA  6  rCH  1  120.00  2 180

rCC = 1.400
rCH = 1.080

connect 1 6

oplsaa.ff
    • the first atom CA is at the center
    • the second atom CA is connected to the first one by a bond with length of rCC
    • the third atom CA is connected to the second one by a bond with length of rCC, forming an angle of 120$^\circ$ between 3-2-1 atoms.
    • the fourth atom CA is connected to the third one by a bound with length of rCC, forming an angle of 120$^\circ$ between 4-3-2 atoms and an diherial of 0$^\circ$.
    • etc.
    • in this case cyclic molecules require additional connect records to close rings: connect 1 6.
    • improper dihedrals can be indicated by improper records (note that fftool assumes the central atom of the improper dihedral to be the third in the list).
    • the filename of the force field file (oplsaa.ff) is given at last.

force field file (.ff file)

  • see an example for .ff file in example.
  • Be careful of the units in .ff file:
    • the distance unit is A.
    • the angle unit is deg.
    • the energy unit is KJ/mol (different from Kcal/mol for LAMMPS real units, $1\text{Kcal}\approx4.184\text{KJ}$)
    • the unit of spring constant for harmonic bonds is kJmol-1A-2
    • the unit of spring constant for harmonic angles is kJmol-1rad-2
  • Be careful of the formula of harmonic potential in .ff file:
    • bond and angle force constants are in the form $k/2 (x - x_0)^2$ (different from that of LAMMPS in which it is $k (x - x_0)^2$).
  • manual editing of the files is usually necessary in order to match the atom names with those of the force field.

use fftool

  • fftool -h gives all help information.
  • An example to build a simulation box with 40 ethanol and 300 water molecules and a density of 38.0 mol/L:
    • fftool 40 ethanol.zmat 300 spce.zmat -r 38.0 -c # -c put the center of box in the origin
    • packmol < pack.inp
    • fftool 40 ethanol.zmat 300 spce.zmat -r 38.0 -c -l # -l for creating inital files for LAMMPS