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Subsections

Constraints and Restraints


Bond constraint parameters

Position restraint parameters

The following describes the parameters for the position restraints feature of NAMD. For historical reasons the term ``constraints'' has been carried over from X-PLOR. This feature allows a restraining potential to each atom of an arbitrary set during the simulation.

Group position restraint parameters

The following describes the parameters for the group position restraints feature of NAMD. Please note that this feature is only available in GPU-resident version of NAMD (NAMD3). This feature allows restraining the center of mass (COM) of a group of atoms to a reference position or another COM of group of atoms, during the simulation.
The restraining potential is defined as:

$\displaystyle E_{\text{restraint}}$ $\displaystyle = k \times \left( \mathbf{\xi} - \mathbf{{\xi}_0} \right)^n$    
$\displaystyle \mathbf{\xi}$ $\displaystyle = \begin{cases}\overrightarrow{r}^{\text{COM}}_{2} - \overrightar... ...{\text{COM}}_{1} \right \rVert & \text{if using distance magnitude} \end{cases}$    
$\displaystyle \mathbf{{\xi}_0}$ $\displaystyle = \begin{cases}\overrightarrow{r}^{\text{center}}_{\text{restrain... ...text{restraint}} \right \rVert & \text{if using distance magnitude} \end{cases}$    

where $ k$ is restraint force constant defined by groupResK and $ n$ is the restraint exponent defined by groupResExp.
$ \mathbf{\xi}$ is the distance vector or length that connects the COM of group 1 to the COM of group 2. In case of defining a reference position for COM of group 1 (group1RefPos), $ \mathbf{\xi}$ specifies the distance vector or length that connects the reference position to the COM of group 2.
$ \mathbf{{\xi}_0}$ is the restraint center vector defined by groupResCenter. $ \mathbf{\overrightarrow{r}^{\text{COM}}_{2}}$ is calculated COM for the atoms in group 2, where atom indices are defined in group2File or group2List. $ \mathbf{\overrightarrow{r}^{\text{COM}}_{1}}$ is either the reference position defined by group1RefPos or calculated COM for the atoms in group 1, where atom indices are defined in group1File or group1List.

Once group position restraints are activated, NAMD outputs additional restraints information for each restraint group. With the frequency of energy outputs, NAMD prints the following fields:
RES_TITLE: TS GROUP_NAME DISTANCE.X DISTANCE.Y DISTANCE.Z FORCE.X FORCE.Y FORCE.Z ENERGY where "TS", "GROUP_NAME", "DISTANCE", "FORCE", "ENERGY" is timestep, assigned tag for the group restraint, distance vector (Å) $ \mathbf{\overrightarrow{r}^{\text{COM}}_{2}} - \mathbf{\overrightarrow{r}^{\text{COM}}_{1}}$ , applied restraint force (kcal/mol $ \times$ Å) along $ \frac{\mathbf{\overrightarrow{r}^{\text{COM}}_{2}} - \mathbf{\overrightarrow{r... ...tarrow{r}^{\text{COM}}_{2} - \overrightarrow{r}^{\text{COM}}_{1} \right \rVert}$ , and restraint energy (kcal/mol), respectively.

Fixed atoms parameters

Atoms may be held fixed during a simulation. NAMD avoids calculating most interactions in which all affected atoms are fixed unless fixedAtomsForces is specified.

Extra bond, angle, and dihedral restraints

Additional bond, angle, and dihedral energy terms may be applied to system, allowing secondary or tertiary structure to be restrained, for example. Extra bonded terms are not considered part of the molecular structure and hence do not alter nonbonded exclusions. The energies from extra bonded terms are included with the normal bond, angle, and dihedral energies in NAMD output.

All extra bonded terms are harmonic potentials of the form $ U(x) = k (x-x_{ref})^2$ except dihedrals and impropers with a non-zero periodicity specified, which use $ U(x) = k (1 + cos(n x - x_{ref}))$ . The only difference between dihedrals and impropers is the output field that their potential energy is added to.

Due to a very old bug all NAMD releases prior to 2.13 have used the MARTINI cosine-based angle potential function for all extra angles. Since workflows may unknowingly depend on this undocumented behavior, cosine-based angles remain the default, but a warning is printed unless the desired behavior is specified via the new option extraBondsCosAngles (defaults to ``on'', set to ``off'' to use the normal harmonic angle potential function for all extra angles).

The extra bonded term implementation shares the parallel implementation of regular bonded terms in NAMD, allowing large numbers of extra terms to be specified with minimal impact on parallel scalability. Extra bonded terms do not have to duplicate normal bonds/angles/dihedrals, but each extra bond/angle/dihedral should only involve nearby atoms. If the atoms involved are too far apart a bad global bond count will be reported in parallel runs.

Extra bonded terms are enabled via the following options:

The extra bonds file(s) should contain lines of the following formats:

In all cases <atom> is a zero-based atom index (the first atom has index 0), <ref> is a reference distance in Å (bond) or angle in degrees (others), and <k> is a spring constant in the potential energy function $ U(x) = k (x-x_{ref})^2$ or, for dihedrals and impropers with periodicity <n> specified and not 0, $ U(x) = k (1 + cos(n x - x_{ref}))$ . Note that $ x_{ref}$ is only a minimum for the harmonic potential; the sinusoidal potential has minima at $ (x_{ref} + 180)/n + i \times 360/n$ .

Use of wall implements a harmonic wall potential similar to the Colvars harmonic wall restraint. The potential function is

\begin{displaymath} U(x) = \begin{cases} k(x-x_{\text{upper}})^2, &\text{if $x ... ...ext{lower}})^2, &\text{if $x < x_{\text{lower}}$} \end{cases}. \end{displaymath}

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Next: Generalized Born Implicit Solvent Up: Force Field Parameters Previous: MARTINI Residue-Based Coarse-Grain Forcefield   Contents   Index
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