Read force parameters¶

Force field format¶

Force field for non-boned interactions:

<pair_params>
particle_type1  particle_type2  epsilon  sigma  alpha
</pair_params>

For bond, angle, and dihedral interactions:

<bond_params>
bond_type  spring_constant  equilibrium_length  function_type
</bond_params>

<angle_params>
angle_type  spring_constant  equilibrium_length  function_type
</angle_params>

<dihedral_params>
dihedral_type  parameter1  parameter2 ...  function_type
</dihedral_params>

For bond constraint and virtual site:

<constraint_params>
constraint_type  equilibrium_length  function_type
</constraint_params>

<vsite_params>
virtual_site_type  a  b  c  function_type
</vsite_params>

An example of force field file:

<pair_params>
Qa Qa 2.3 0.6 1.0
Qa Q0 2.0 0.6 1.0
Qa Na 0.5 0.47 1.0
Qa C4 0.5 0.47 1.0
Qa C1 2.0 0.62 1.0
Qa SC3 0.5 0.47 1.0
Qa SC1 2.0 0.62 1.0
Qa SP1c 2.7 0.47 1.0
Q0 Q0 2.0 0.6 1.0
Q0 Na 0.5 0.47 1.0
Q0 C4 0.5 0.47 1.0
Q0 C1 2.0 0.62 1.0
Q0 SC3 0.5 0.47 1.0
Q0 SC1 2.0 0.62 1.0
Q0 SP1c 2.7 0.47 1.0
Na Na 2.3 0.47 1.0
Na C4 2.7 0.47 1.0
Na C1 2.7 0.47 1.0
Na SC3 2.7 0.47 1.0
Na SC1 2.7 0.47 1.0
Na SP1c 2.3 0.47 1.0
C4 C4 4.5 0.47 1.0
C4 C1 4.0 0.47 1.0
C4 SC3 4.5 0.47 1.0
C4 SC1 4.0 0.47 1.0
C4 SP1c 2.7 0.47 1.0
C1 C1 4.5 0.47 1.0
C1 SC3 4.5 0.47 1.0
C1 SC1 4.5 0.47 1.0
C1 SP1c 2.3 0.47 1.0
SC3 SC3 3.4 0.43 1.0
SC3 SC1 3.4 0.43 1.0
SC3 SP1c 2.7 0.47 1.0
SC1 SC1 3.4 0.43 1.0
SC1 SP1c 2.3 0.47 1.0
SP1c SP1c 2.3 0.47 1.0
</pair_params>

<constraint_params>
SP1c-SC3 0.4904 1
SP1c-SC1 0.6019 1
SC3-SC1 0.2719 1
SC1-SC3 0.7237 1
SC1-SC1 0.5376 1
</constraint_params>

<vsite_params>
SC1-SC1-SC3-SC1 0.9613 0.6320 0.0 1
SC1-SC3-SP1c-SC1 0.5207 0.2882 -1.03168 4
SC1-SC1-SC3-SC1_1 0.2287 0.4111 1.41920 4
</vsite_params>

<bond_params>
Q0-Qa 1250.0 0.450 1
Qa-Na 1250.0 0.450 1
Na-Na 1250.0 0.370 1
Na-C1 1250.0 0.480 1
C1-C1 1250.0 0.480 1
C1-C4 1250.0 0.480 1
C4-C4 1250.0 0.480 1
C4-C1 1250.0 0.480 1
SC1-C1 1250.0 0.425 1
</bond_params>

<angle_params>
Qa-Na-Na 25.0 120.000 2
Qa-Na-C1 25.0 180.000 2
Na-C1-C1 35.0 180.000 2
C1-C1-C1 35.0 180.000 2
Na-C1-C4 35.0 180.000 2
C1-C4-C4 20.0 95.000 2
C4-C4-C1 45.0 120.000 2
SC1-SC1-C1 25.0 180.0 2
</angle_params>

<dihedral_params>
SP1c-SC3-SC1-SC1_F2 -179.7 50.0 2
</dihedral_params>

Use force fields¶

Description:

Force fields in the format could be read by force_field_gala module. The classes of force_field_gala module are listed as following.

class LJCoulombShiftForce(all_info, nlist, rcut, rshift, epsilon_r, file)¶

Constructor of an object to simutaneously calculate modified Lennard-Jones and Coulomb interactions which are smoothed by a shift function same to GROMACS.

Parameters:

all_info (AllInfo) – System information.
nlist (NeighborList) – Neighbor list.
rcut (float) – Cut-off radius.
rshift (float) – Shift radius.
epsilon_r (float) – Relative dielectric constant.
file (string) – Force field file.

Example:

import force_field_gala
e_r = 15.0
lj = force_field_gala.LJCoulombShiftForce(all_info, nlist, 1.2, 0.9, e_r, "Equ.force_field")
app.add(lj)

class LJEwaldForce(all_info, nlist, rcut, file)¶

Constructor of an object to simutaneously calculate Lennard-Jones and the short-part Coulomb interactions.

Parameters:

all_info (AllInfo) – System information.
nlist (NeighborList) – Neighbor list.
rcut (float) – Cut-off radius.
file (string) – Force field file.

setEnergy_shift()¶: calls the function to shift LJ potential to be zero at cut-off point.

setDispVirialCorr(bool open)¶: switches the dispersion virial correction.

Example:

import force_field_gala
lj = force_field_gala.LJEwaldForce(all_info, neighbor_list, 1.0, "ffnonbonded.force_field")
lj.setEnergy_shift()
lj.setDispVirialCorr(True)#dispersion virial correction
app.add(lj)

class BondForceHarmonic(all_info, file)¶

Constructor of an object to calculate harmonic bond interactions.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

Example:

bondforce = force_field_gala.BondForceHarmonic(all_info, "ffbonded.force_field")
app.add(bondforce)

class AngleForceHarmonicCos(all_info, file)¶

Constructor of an object to calculate harmonic cosine angle interactions.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

Example:

angleforce = force_field_gala.AngleForceHarmonicCos(all_info, "ffbonded.force_field")
app.add(angleforce)

class AngleForceHarmonic(all_info, file)¶

Constructor of an object to calculate harmonic angle interactions.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

Example:

angleforce = force_field_gala.AngleForceHarmonic(all_info, "ffbonded.force_field")
app.add(angleforce)

class DihedralForceAmberCosine(all_info, file)¶

Constructor of an object to calculate Amber cosine dihedral interactions.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

Example:

dihedralforce = force_field_gala.DihedralForceAmberCosine(all_info, "ffbonded.force_field")
app.add(dihedralforce)

class DihedralForceHarmonic(all_info, file)¶

Constructor of an object to calculate harmonic dihedral interactions.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

Example:

dihedralforce = force_field_gala.DihedralForceHarmonic(all_info, "ffbonded.force_field")
app.add(dihedralforce)

class BondConstraint(all_info, file)¶

Constructor of an object to implement bond constraints.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

setNumIters(int ncycles)¶: specifies the number of iterations of calcuation.

setExpansionOrder(int order)¶: specifies the spread order.

Example:

bond_constraint = force_field_gala.BondConstraint(all_info, "Equ.force_field")
bond_constraint.setExpansionOrder(4)
bond_constraint.setNumIters(1)
app.add(bond_constraint)

class Vsite(all_info, file)¶

Constructor of an object to implement virtual sites using a same method to GROMACS.

Parameters:

all_info (AllInfo) – System information.
file (string) – Force field file.

Example:

vs = force_field_gala.Vsite(all_info, "Equ.force_field")
app.add(vs)

Use GROMACS force fields¶

Description:

Force fields in GROMACS format are supported by force_field_itp module. The usage and methods are same to force_field_gala module, but for reading the force fields in GROMACS format from itp files.

An example:

import force_field_itp
lj = force_field_itp.LJEwaldForce(all_info, neighbor_list, 1.0, "ffnonbonded.itp")
lj.setEnergy_shift()
lj.setDispVirialCorr(True)#dispersion virial correction
app.add(lj)

Convert GROMACS files¶

Description:

Convert GROMACS files to GALA files including configuration and force fields by gro_to_xml module. Execution command is python gro_to_xml.py with two necessary parameters --gro= and --top= to set the GROMACS file names.

An example:

python gro_to_xml.py --top=Topol.top --gro=Equ.gro

Then two files ‘Equ.xml’ of configuration and ‘Equ.force_field’ of force field will be generated.