STM:Client

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An STM client is a biased molecular dynamics simulation that provides the mean forces and metric tensor for a specific bead along the string path. To perform an STM path-optimisation step, this information must be collected from all clients, i.e. from all beads.

Because the computational resources required by a single client may be substantial, especially for systems described using hybrid QM/MM methods, STM clients can be launched in two modes: either all at once in a coordinated manner, known as synchronous mode, or as independent jobs launched by the STM server, known as asynchronous mode. For further details, see STM:Server.

Configuration

• STM:Client Controls
• STM:Collective variables

IMPORTANT

• Collective variables must be specified in the same order as on the string server.
• The total duration of the STM client simulation (AMBER: specified by nstlim as a total number of integration steps) must be long enough to satisfy all requests from the STM server.

Implementation Details

The STM client biases the system using harmonic restraints applied to individual collective variables:

$E({\xi }_i(t))=\frac{1}{2}{K}_i{({\xi }_i(t)-{\xi }_{i,0})}^2(1)$

where ${\xi }_i(t)$ is the instantaneous value of the collective variable, $K_i$ is the force constant, and ${\xi }_{i,0}$ is the bead position specified by the STM server.

The mean forces and metric tensor are accumulated as time averages:

$\frac{\partial A(\mathit{\xi })}{\partial {\xi }_{i,0}}=-\frac{1}{N_s}\sum _{t=1}^{N_s}{K}_i({\xi }_i(t)-{\xi }_{i,0})(2)$

$M_{ij}=\frac{1}{N_s}\sum _{t=1}^{N_s}\left(\sum _{k=1}^{N_a}\frac{\partial {\xi }_i(t)}{\partial x_k}\frac{\partial {\xi }_j(t)}{\partial x_k}\right)(3)$

where $N_s$ is the number of sampled MD steps, $N_a$ is the number of atoms, and $x_k$ denotes the Cartesian coordinates of the system.

The values of $N_s$ and ${\xi }_{i,0}$ are set by the STM server together with the requested client mode:

• I — initialisation
• A — accumulation
• E — equilibration
• P — production

In the I and E modes, the restraint centres, ${\xi }_{i,0}$, are gradually moved towards their target values. After reaching the target values, they are held fixed for the steady part of the stage, whose length is controlled by the steadylen fraction of $N_s$. In the A and P modes, the mean forces and metric tensor are sampled at target values and reported to the STM server. Once all data are collected, the path is updated, and the procedure is repeated with new bead positions.