groio

November 18, 2022 · View on GitHub

Files with the gro file extension contain a molecular structure in Gromos87 format. gro files can be used as trajectory by simply concatenating files.

Two water molecules, t= 0.0
    6
    1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
    1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
    1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
    2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
    2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
    2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
   1.82060   1.82060   1.82060

Lines contain the following information (top to bottom):

title string (free format string, optional time in ps after 't=')
number of atoms (free format)
one line for each atom (fixed format):
- residue number
- residue name
- atom name
- atom number
- position (in nm, x y z in 3 columns)
- velocity (in nm/ps (or km/s), x y z in 3 columns)
box vectors (free format, space separated reals), values: vx, vy, bz

Fortran format: (i5,2a5,i5,3f8.3,3f8.4)

For more information please see reference.

`gro_open`

Open file for reading and checked. Frame offset table is constructed (byte position where frame starts). Move to selected frame with fseek. If the function fails stat is a positive number, otherwise it is set to zero. If stat is not present end error occurs error stop is raised.

call gro_open (file, unit, nframes, offset, stat, errmsg)

Parameters

character(*), intent(IN) :: file

Input file name.

integer, intent(OUT) :: unit

Fortran file unit.

integer, intent(OUT) :: nframes

Number of frames in file.

integer(INT64), allocatable, dimension(:), intent(INOUT) :: offset

Frame offset table. Array size same as nframes.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`gro_close`

Close opened file.

call gro_close (unit, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`glo_read_header`

Read file header in GRO format.

call gro_read_header (unit, comment, natoms, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

character(*), intent(OUT) :: comment

Comment string. Optional time in ps after t=.

integer, intent(OUT) :: natoms

Number of atoms.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`gro_read_data`

Read data in GRO format.

call gro_read_data (unit, natoms, atomi, atomn, resi, resn, coor, box, vel, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

integer, intent(OUT) :: atomi, resi

Atom and residue index.

character(*), intent(OUT) :: atomn, resn

Atom and residue name.

real, dimension(DIM,natoms), intent(OUT) :: coor

Atom cartesian coordinates in nm.

real, dimension(DIM,DIM), intent(OUT) :: box

Simulation box dimensions in nm.

real, dimension(DIM,natoms), intent(OUT), optional :: vel

Atom velocity in nm/ps.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`gro_read_coor`

Read ONLY coordinate data in GRO format.

call gro_read_coor (unit, natoms, coor, box, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

real, dimension(DIM,natoms), intent(OUT) :: coor

Atom cartesian coordinates in nm.

real, dimension(DIM,DIM), intent(OUT) :: box

Simulation box dimensions in nm.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`gro_skip_data`

Read through file (skip) in GRO format but do not store any data.

call gro_skip_data (unit, natoms, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`gro_write`

Write data in GRO format.

call gro_write (unit, comment, natoms, atomi, atomn, resi, resn, coor, box, vel, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

character(*), intent(OUT) :: comment

Comment string.

integer, intent(IN) :: natoms

Number of atoms.

integer, intent(IN) :: atomi, resi

Atom and residue index.

character(*), intent(IN) :: atomn, resn

Atom and residue name.

real, dimension(DIM,natoms), intent(IN) :: coor

Atom cartesian coordinates in nm.

real, dimension(DIM,DIM), intent(IN) :: box

Simulation box dimensions in nm.

real, dimension(DIM,natoms), intent(IN), optional :: vel

Atom velocity in nm/ps.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

Example

Example of reading GRO file.

program main
  use atomlib_groio
  use iso_fortran_env, only: INT64
  implicit none
  integer, parameter :: DIM = 3
  integer, allocatable :: atomi(:), resi(:)
  character(6), allocatable :: atomn(:), resn(:)
  real, allocatable :: coor(:,:)
  integer(INT64), allocatable :: offset(:)
  character(128) :: comment
  real :: box(DIM,DIM)
  integer :: unit, natoms, nframes, status

  call gro_open ("conf.gro", unit, nframes, offset, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call gro_read_header (unit, comment, natoms, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  allocate (atomi(natoms), resi(natoms), atomn(natoms), &
  & resn(natoms), coor(DIM,natoms), STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call gro_read_data (unit, natoms, atomi, atomn, resi, resn, coor, box, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call gro_close (unit, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message  

end program main