File Formats
CudaSPONGE file format reference for SPONGE 1.4.This page was translated by GPT-5.5 AI.
All atom indices are counted from 0.
Control Files
mdin
The first line is the title line and is required
# Text after a hash sign is a comment
# command = value
mode = NVT
thermostat = middle_langevin
# Braces A { B = C } represent A_B = C
middle_langevin
{
gamma = 10
}
# Two hash signs comment out the entire brace block
## amber
{
parm7 = test.parm7
rst7 = test.rst7
}
default_in_file_prefix = exampleCommands in mdin can also be entered on the command line. For example, the above is equivalent to:
SPONGE -mode NVT -thermostat middle_langevin -middle_langevin_gamma 10 -default_in_file_prefix examplecv_in_file
# Text after a hash sign is a comment
# command = value
####################
# Define virtual atoms
####################
com1 # Any name that does not duplicate a built-in keyword
{
vatom_type = center_of_mass
atom = 3 5 7
}
com2
{
vatom_type = center_of_mass
atom = 4 6 9
}
####################
# CV definitions
####################
rmsd_test # Any name that does not duplicate a built-in keyword
{
CV_type = rmsd
atom_in_file = test_atom.txt
coordinate_in_file = test_coordinate.txt
}
nice_day # Any name that does not duplicate a built-in keyword
{
CV_type = angle
atom = com1 3 com2 # A virtual atom name can be used wherever an integer input is required
}
######################
# CV usage
######################
print
{
CV = nice_day rmsd_test
}
restrain
{
CV = rmsd_test
weight = middle_langevin_gamma # Values requiring an integer or floating-point number can use variables from mdin
reference = 0.
}
##meta1d # Double hash signs comment out the entire brace block
{
CV = nice_day
dCV = 0.01
CV_minimal = 0
CV_maximum = 3.14
height = 10
sigma = 0.1
welltemp_factor = 50
}
###################
# System control
###################
dont_check_input = 0Force Field Files
AMBER Format
amber_parm7
amber_rst7
See the AMBER official website.
bond_in_file
Total number of bonds
Atom a Atom b Force constant Equilibrium position
...
Atom a Atom b Force constant Equilibrium positionangle_in_file
Total number of bond angles
Atom a Atom b Atom c Force constant Equilibrium position
...
Atom a Atom b Atom c Force constant Equilibrium positiondihedral_in_file
Total number of dihedrals
Atom a Atom b Atom c Atom d Periodicity Force constant Phase angle
...
Atom a Atom b Atom c Atom d Periodicity Force constant Phase anglenb14_in_file
Total number of nb14 entries
Atom a Atom b LJ scaling factor Electrostatic scaling factor
...
Atom a Atom b LJ scaling factor Electrostatic scaling factorcmap_in_file
Number of cmap types Total number of cmaps
Resolution of cmap type 1 Resolution of cmap type 2 ... Resolution of cmap type x
Parameters for cmap type 1, with Resolution of cmap type 1^2 entries in total
Parameters for cmap type 2, with Resolution of cmap type 2^2 entries in total
...
Parameters for cmap type x, with Resolution of cmap type x^2 entries in total
Atom a Atom b Atom c Atom d Atom e cmap type
...
Atom a Atom b Atom c Atom d Atom e cmap typeLJ_in_file
Number of atoms Number of LJ types
A coefficient for LJ0-LJ0
A coefficient for LJ1-LJ0 A coefficient for LJ1-LJ1
...
A coefficient for LJx-LJ0 A coefficient for LJx-LJ1 ... A coefficient for LJx-LJx
B coefficient for LJ0-LJ0
B coefficient for LJ1-LJ0 B coefficient for LJ1-LJ1
...
B coefficient for LJx-LJ0 B coefficient for LJx-LJ1 ... B coefficient for LJx-LJx
LJ type of atom 1
LJ type of atom 2
...
LJ type of atom ncharge_in_file
A special charge unit is used here so that and no force constant needs to be multiplied. In this unit system, one electron carries a charge of -18.2223.
Number of atoms
Charge of atom 1
Charge of atom 2
...
Charge of atom nresidue_in_file
Number of atoms Number of residues
Number of atoms in residue 1
Number of atoms in residue 2
...
Number of atoms in residue nCustom Force Field Format Files
After providing the force field form definition files below, you must also provide force field parameter files. The force field parameter files follow the standard SPONGE built-in formats described above.
listed_forces_in_file
Defines bonded interactions.
[[[ Name 1 ]]]
[[ parameters ]]
int atom_i, int atom_j, ..., int atom_l, Parameter type (float/int) Parameter name, Parameter type (float/int) Parameter name, ... Parameter type (float/int) Parameter name
[[ potential ]]
Potential energy function
E = f(r_ij, theta_ijk, phi_ijkl)
Here, r_ij denotes the distance between atom_i and atom_j, theta_ijl denotes the corresponding angle, and phi_ijkl denotes the corresponding dihedral angle
[[ connected_atoms ]]
ij (indicates that atoms i and j are connected; used for periodic mapping and automatic constraint-atom detection. Leave this section empty if not needed)
[[ constrain_distance ]]
Name of the parameter representing the constraint distance. Leave this section empty if not needed
[[ end ]]
[[[ Name 2 ]]]
...
[[ end ]]
... ...pairwise_force_in_file
Defines nonbonded interactions.
[[[ Name ]]]
[[ parameters ]]
Parameter type (float/int) Parameter name, Parameter type (float/int) Parameter name, ... Parameter type (float/int) Parameter name
[[ potential ]]
Potential energy function
E = f(r_ij)
[[ with_ele ]]
true/false
[[ electrostatic_potential ]]
Electrostatic potential energy function
E_ele = f(r_ij, q_i, q_j)
[[ end ]]soft_walls_in_file
Defines soft walls.
[[[ Name 1 ]]]
[[ potential ]]
Potential energy function E = f(x, y, z)
[[ end ]]
[[[ Name 2 ]]]
...
[[ end ]]
... ...Coordinate and Velocity File Formats
coordinate_in_file
Input coordinate file.
Number of atoms [timestamp, optional]
x coordinate of atom 1 y coordinate of atom 1 z coordinate of atom 1
x coordinate of atom 2 y coordinate of atom 2 z coordinate of atom 2
... ...
x coordinate of atom n y coordinate of atom n z coordinate of atom n
Length of box x basis vector Length of box y basis vector Length of box z basis vector Angle between box y and z basis vectors Angle between box x and z basis vectors Angle between box x and y basis vectorsvelocity_in_file
Input velocity file. Note that velocities are in SPONGE internal units.
Number of atoms [timestamp, optional]
x velocity of atom 1 y velocity of atom 1 z velocity of atom 1
x velocity of atom 2 y velocity of atom 2 z velocity of atom 2
... ...
x velocity of atom n y velocity of atom n z velocity of atom n