rattle

Jump to Description or Examples; explanation of how commands are documented.

Purpose

The rattle command is used before the dynamics command to set up constraints in bonds, angles, or water molecules in a molecular dynamics simulation. It can be used to constrain bonds or any atom pairs to user-defined distances. It can be used to constrain angles spanned by two constrained bonds. In addition, it can be used to fix the geometry of water molecules so that the fixed-geometry water models SPC and TIP3P can be used in a simulation.

Syntax and Description

The syntax differs slightly, depending on whether bonds, angles, water, or nothing is being constrained:

Constraining bonds or atom pairs

rattle bonds ?-bondLength bondlength_value? ?-tolerance tolerance_value? ?atom1_list atom2_list?

By default, every bond in the system is constrained to its current length if the rattle bonds command is issued without the optional keywords and values.

-bondLength bondlength_value specifies the interatomic distance to which the atom pairs are constrained.

-tolerance tolerance_value specifies the tolerance with which the constraints are enforced.

atom1_list atom2_list are two sets of atom specifications which identify the atom pairs to be constrained.

Constraining angles

rattle angles ?-angleValue angle_value? ?-tolerance tolerance_value? ?atom1_list atom2_list atom3_list?

The roles of the optional keywords in the rattle angles command are analogous to those of -bondLength, -tolerance, and the atom lists in the rattle bonds command.

By default, every angle in the system is constrained to its current value.

Note, however, that the rattle angles command actually constrains the distance between the 1,3 atoms of an angle. Therefore, you need to issue the rattle bonds command before the rattle angles command to constrain the bond distances so that the angle itself can be constant.

Constraining water geometry

rattle water ?-waterType SPC|TIP3P|CURRENT? ?-tolerance tolerance_value?

By default, water molecules are constrained to their current positions, using the CURRENT water model. However, when the SPC or TIP3P models are specified, the water molecules are constrained to their equilibrium geometry according to that model. The nonbond parameters are also changed to the values used in the specified water model.

Turning rattle off

rattle off

This command clears all constraints set up by previous rattle commands. Notice that this command is also needed when you want to change the rattle parameters from those used in previous dynamics stages (for example, to rattle angles in addition to bonds). You have to turn rattle off first and then issue new rattle commands to change these parameters.

Example 1

Jump to Syntax or Description

rattle bonds -bondLength 1.0000 -tolerance 1e-4 "*:WTR_*:H11" "*:WTR_*:O1"

All the bonds between H11 and O1 in residues WTR of all molecules in a box of water molecules are constrained to bond lengths of 1.0 Å during dynamics, with a tolerance of 1e-4 Å.

Example 2

rattle angles -angleValue 109.0 \
        -tolerance 1e-4 "*:WTR_*:H11" "*:WTR_*:O1" "*:WTR_*:H12"

All the angles formed by H11, O1, and H12 in residues WTR of all molecules are constrained to an angle of 109° during dynamics, with a tolerance of 1e-4°.

Example 3

rattle water -waterType SPC -tolerance 1e-4

All the water molecules are maintained at the fixed geometry of the SPC model during dynamics, with a tolerance of 1e-4. Furthermore, the nonbond parameters used for water are changed to those of the SPC model.

This command also makes use of the molGeom command to fix the geometry of the water molecules.

Example 4

rattle water -waterType CURRENT -tolerance 1e-4

All water molecules are maintained at the current geometry during dynamics. The current forcefield is used for water.

Example 5

rattle bonds

Constrain all bonds in molecules to the current bond lengths. The tolerance is set at the default of 1e-5 Å.

Main access page

Advanced-Use access.

List of BTCL commands pseudoAtom command readFile command