Gromacs simulation

Currently, the engine code available in NEXTMOL Modeling is GROMACS3. It allows you to perform several simulations operations, such as energy minimization, NPT, NVT, and more.

There are two types of parameters: main and expert. To edit the expert parameters, click on Show expert parameters.

Allowed number of parents: 1

Run parameters

Run parameters are the most important parameters to define the basic setup of the run.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Calculation mode

Indicate what Gromacs should do: Molecular Dynamics (MD) or Energy Minimization (EM)

selector

md, steep

MD

N/A

Number of steps

Maximum number of steps for the MD integration or energy minimization

integer

>0

50000

N/A

Time step

Time step for the MD integration (only for MD)

float

0 < x < 0.01

0.002

ps

Convergence criterion for EM

The convergence criterion (on the forces) for the energy minimization (only for EM)

float

0 <x<10000

100

kJ mol-1nm-1

Initial step size for EM

The initial step size for the energy minimization (only for EM)

float

0 <x <0.1

0.01

nm

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Remove the center of mass (COM) motion

Indicate whether and how the center of mass motion should be removed

selector

linear, angular, none

linear

N/A

Frequency for COM motion removal

Indicate the step frequency for the removal of the COM motion

integer

integer

100

N/A

Output control

Parameters controlling the output of the simulation

Main parameters

Parameter Description Value type Value restrictions Default value Units

Frequency for trajectory writing

Indicate the step frequency for the writing of the coordinates to the trajectory

integer

≥0

500

steps

Frequency for energy writing

Indicate the step frequency for the writing of the energy terms

integer

≥0

100

steps

Frequency for log writing

Indicate the step frequency for the writing of the log file

integer

> 0

500

steps

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Frequency for velocity writing

Indicate the step frequency for the writing of the velocities to the trajectory

integer

≥0

0

steps

Frequency for forces writing

Indicate the step frequency for the writing of the forces to the trajectory

integer

≥0

0

steps

Frequency for energy calculation

Indicate the number of steps that elapse between calculating the energies

integer

≥0

100

steps

Electrostatics

Parameters controlling the electrostatics and Van der Waals interactions of the simulation.

Please choose Van der Waals (VdW) calculation mode = Cut-off for best performance (this is due to the fact that the platform runs with GPU instances).

Main parameters

Parameter Description Value type Value restrictions Default value Units

Electrostatics calculation mode

Indicate how the electrostatic interactions shall be calculated

selector

Cut-off, PME

PME

N/A

Van der Waals (VdW) calculation mode

Indicate how the Van der Waals interactions shall be calculated

selector

Cut-off, PME

Cut-off

N/A

Coulomb cutoff

Distance for the Coulomb cut-off

float

0< x < 10

1.0

nm

VdW cutoff

Distance for the VdW cut-off

float

0< x < 10

1.0

nm

Fourier grid spacing

Fourier-space grid spacing

float

0< x < 1

0.12

nm

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Combination rules for VdW parameters

The combination rules to combine VdW parameters in the reciprocal part of VdW-PME (onlv for VdW calculation mode = PME)

selector

Geometric, Lorentz-Berthelot

Geometric

N/A

Relative strength of the Ewald-shifted direct potential at rcoulomb

Indicates the relative strength of the Ewald-shifted direct potential at rcoulomb (only for Electrostatics calculation mode = PME)

float

0 <x <0.1

1.e-5

N/A

Relative strength of the dispersion potential at rvdw

Indicates the relative strength of the dispersion potential potential at rvdw (only for VdW calculation mode = PME)

float

0 <x <0.1

1.e-3

N/A

Relative dielectric constant

The relative dielectric constant. A value of 0 means infinity.

float

≥0

1.0

N/A

PME interpolation order

Interpolation order for PME. 4 equals cubic interpolation.

integer

0 <x<12

4

N/A

Apply dispersion corrections

Indicate whether dispersion corrections shall be applied

selector

no, Ener, EnerPres

no

N/A

Shift VdW potential

Indicate whether the VdW potential shall be shifted by a constant such that is it zero at the cutoff

selector

potential_shift, none

potential_shift

N/A

Thermostat

Parameters controlling the temperature coupling of the system (thermostat).

Main parameters

Parameter Description Value type Value restrictions Default value Units

Temperature coupling mode

Indicate whether a temperature coupling shall be applied, and how

selector

no, berendsen,nose-hoover, v_rescale

no

N/A

Reference temperature

Indicate the reference temperature for the coupling (only for temperature coupling mode not no)

float

>0

300

K

Time constant for coupling

Indicate the time constant for the temperature coupling (only for temperature coupling mode not no)

float

>0

1.0

ps

Generate initial random velocities

Indicate whether to assign the initial velocities from a random Maxwell distribution (otherwise they are taken from the input file)

boolean

True, False

TRUE

N/A

Temperature for Maxwell distribution

Indicate the temperature for the Maxwell distribution (only for Generate initial random velocities = True)

float

≥0

300

K

Barostat

Parameters controlling the pressure coupling of the system (barostat).

Main parameters

Parameter Description Value type Value restrictions Default value Units

Pressure coupling mode

Indicate whether a pressure coupling shall be applied, and how

selector

no, berendsen, parrinello-rahman

no

N/A

Pressure coupling isotropy

Indicate the kind of isotropy of the applied pressure coupling

selector

isotropic, semiisotropic, anisotropic

isotropic

N/A

Reference pressure

Indicate the reference pressure for the isotropic coupling

float

>0

1.0

bar

Reference pressure (x ∕ y, z)

Indicate the reference pressure for the semiisotropic coupling (x ∕ y, z)

float

>0

1.0

bar

Reference pressure (x, y, z)

Indicate the reference pressure for the anisotropic coupling (x, y, z)

float

>0

1.0

bar

Time constant for coupling

Indicate the time constant for the pressure coupling

float

>0

1.0

ps

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Compressibility

Indicate the compressibility pressure for the isotropic coupling

float

>0

4.5e-5

bar-1

Compressibility (x ∕ y, z)

Indicate the compressibility pressure for the semiisotropic coupling (x ∕ y, z)

float

>0

4.5e-5

bar-1

Compressibility (x, y, z)

Indicate the compressibility pressure for the anisotropic coupling (x, y, z)

float

>0

4.5e-5

bar-1

Scale the reference coordinates for position restraints

Indicate whether and how the reference coordinates for position restraints shall be scaled

selector

no, all, com

com

N/A

Bonds

Parameters controlling the bonds.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Bond constraints mode

Indicate whether bond constraints shall be applied, and how

selector

none, h_bonds, all_bonds, h_angles, all_angles

h_bonds

N/A

Constraint algorithm

Indicate the algorithm used for the constraints

selector

lincs, shake

LINCS

N/A

Expert parameters

Parameter Description Value type Value restrictions Default value Units

LINCS order

Indicate the highest order in the expansion of the constraint coupling matrix

integer

0 <x < 20

4

N/A

LINCS iterations

Indicate the number of iterations to correct for rotational lengthening in LINCS

integer

0 <x < 10

1

N/A

LINCS warning angle

Indicate the maximum angle that a bond can rotate before LINCS will complain

float

0 <x < 360

30

N/A

PBC and Neighbor Search

Parameters controlling the periodic boundary conditions and the neighbor search.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Periodic boundary conditions

Indicate the periodic boundary conditions

selector

xyz, xy, no

xyz

N/A

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Molecules coupling to themselves through periodic BC

Indicate whether there are molecules that couple to themselves through periodic BC. Implies a slower PBC algorithm.

boolean

True, False

False

N/A

Frequency to update the neighbor list

Indicate the step frequency to update the neighbor list

integer

≥0

10

N/A

Method to search for neighbors

Method to check the atoms when constructing a new neighbor list. Grid search is more efficient than simple search for large systems

selector

grid, simple

grid

N/A

Verlet buffer tolerance

Indicate the maximum allowed error for pair interactions per particle caused by the Verlet buffer, which indirectly sets rlist

float

>0

0.005

kJmol-1ps-1

Cut-off distance for the shortrange neighbor list

Indicate the cut-off distance for the shortrange neighbor list

float

>0

1.0

N/A

SMD

Parameters controlling Steered Molecular Dynamics (SMD) simulations. Enabling this option applies a pulling force to a selected group of atoms. You can define this selection in several ways:

  1. Distance – pulls along the vector connecting the centers of mass of two atom groups.

  2. Direction and

  3. Direction Periodic – by default, these use only one atom group, although you can specify two.

In all cases, the pulling force is applied to the first group.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Perform SMD

Indicate whether SMD shall be performed

selector

yes, no

no

N/A

Definition of the pulling direction

Indicate how the pulling direction shall be defined

selector

distance,direction,direction-periodic

distance

N/A

The pulling direction

Indicate the pulling direction

float

any float

[0, 0, 0]

N/A

Select the dimension the pulling acts on

Selects the dimensions that this pull coordinate acts on and that are printed to output file. For instance, [False, False, True] only calculates the distance in the z-direction

boolean

yes, no

[no, no, yes]

Pulling velocity

Indicate the pulling velocity

float

any float

0.0001

nm/ps

Force constant for the pulling

Indicate the force constant for the pulling

float

any float

2000

kJmol-1nm-2

First SMD pulling group

Indicate the name of the first SMD pulling group

string

N/A

Group1

N/A

Component name of first group

Indicate the component name of the atoms in the first group

selector_component

component types, “all”

0

N/A

Atom name of first group

Indicate the atom name of the atoms in the first group

selector_atom

atom_types, “all”

0

N/A

x range of first group

Indicate the x range of the atoms in the first group

float

any float

[-10000, 10000]

Angstrom

y range of first group

Indicate the y range of the atoms in the first group

float

any float

[-10000, 10000]

Angstrom

z range of first group

Indicate the z range of the atoms in the first group

float

any float

[-10000, 10000]

Angstrom

Second SMD pulling group

Indicate the name of the second SMD pulling group

string

N/A

Group2

N/A

Component name of second group

Indicate the component name of the atoms in the second group

selector_component

component types, “all”

0

N/A

Atom name of second group

Indicate the atom name of the atoms in the second group

selector_atom

atom_types, “all”

0

N/A

x range of second group

Indicate the x range of the atoms in the second group

float

any float

[-10000, 10000]

Angstrom

y range of second group

Indicate the y range of the atoms in the second group

float

any float

[-10000, 10000]

Angstrom

z range of second group

Indicate the z range of the atoms in the second group

float

any float

[-10000, 10000]

Angstrom

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Frequency for writing pulling positions

Indicate the step frequency for writing the pulling positions

integer

≥0

50

N/A

Frequency for writing pulling forces

Indicate the step frequency for writing the pulling forces

integer

≥0

50

N/A

Write averaged coordinates

Indicate whether to write the averaged (since last output) or the instantaneous coordinates

boolean

yes, no

no

N/A

Write averaged forces

Indicate whether to write the averaged (since last output) or the instantaneous forces

boolean

yes, no

no

N/A

Position Restraints

Parameters controlling the position restraints. It can be defined up to four position restraints.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Component name

The component name of the atoms to be restrained

selector_component

component types, “all”

0

N/A

Atom name

The atom name of the atoms to be restrained

selector_atom

atom_types, “all”

0

N/A

Force constant

Indicate the force constant for the restraining potential

float

≥0

PME

kJ mol-1 m-2

Simulated Annealing

Parameters controlling the Simulated Annealing.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Simulated Annealing mode

Indicate whether a Simulated Annealing simulation shall be performed

selector

no, single

no

N/A

Simulation time at annealing points

Indicate the simulation time at the annealing points

float

≥0

0

ps

Temperature at annealing points

Indicate the temperature at the annealing points

float

>0

300

K

Potential Walls

Parameters controlling the Potential Walls simulations.

Main parameters

Parameter Description Value type Value restrictions Default value Units

Number of walls

When set to 1 there is a wall at z=0, when set to 2 there is also a wall at z=z-box

selector

0, 1, 2

0

N/A

Type of potential wall

9-3 (LJ 9-3 integrated over the volume behind the wall), 10-4 (LJ 10-4 integrated over the wall surface), 12-6 (direct LJ potential with the z distance from the wall)

selector

9-3, 10-4, 12-6

9-3

N/A

Number density of atoms for wall

The number density of the atoms for each wall

float

≥0

N/A

[nm-3] / [nm-2]

Atom type name in force-field

Name for the wall atom type in the force field. It will inserted automatically in the topology file for the run

str

N/A

N/A

N/A

Sigma of the atom type

Sigma of the atom type, necessary to define the potential

float

N/A

N/A

nm

Epsilon of the atom type

Epsilon of the atom type, necessary to define the potential

float

N/A

N/A

kJ/mol

Linear potential continuation beyond wall

Below this distance from wall the potential is continued linearly and thus the force is constant. Setting to a positive value is useful for equilibrations with atoms beyond wall

float

N/A

N/A

nm

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Scaling factor for the third box vector

For Ewald summation only. Can only be used with nwall=2, where one should use ewald-geometry=3dc. The empty layer in the box serves to decrease the unphysical Coulomb interaction between periodic images

float

≥2

3

N/A

Mass of the atom type

Mass of the atom type

float

N/A

N/A

atomic unit (u)

Charge of the atom type

Charge of the atom type

float

N/A

N/A

electrons (e)

Acceleration

In some specific cases, a system may be better represented in non-equilibrium conditions. For such cases, the acceleration option allows to define a group of atoms that will undergo constant acceleration through the application of an external force. The following settings allow to configure the selection of atoms and the magnitude of acceleration.

Parameter Description Value type Value restrictions Default value Units

Perform acceleration

Indicate whether acceleration is activated or not

selector

yes, no

no

N/A

Name of the acceleration group

User-defined name of the group of atoms to be accelerated

string

N/A

Group Acceleration

N/A

Component name of reference atom

Indicate the component name of the reference atom

selector_component

component types, “all”

all

N/A

Residue name of reference atom

Indicate the residue name of the reference atom

selector_residue

residue types, “all”

all

N/A

Atom type of reference atom

Indicate the component name of the reference atom

selector_atom_type

atom_types, “all”

all

N/A

Atom name of reference atom

Indicate the atom name of the reference atom

selector_atom

atom_names, “all”

all

N/A

Acceleration

Value of the acceleration applied on the selection

Float

≥0

0

nm/ps2