Module: isdb
| Description | Usage |
|---|---|
| tools for doing integrative structural and dynamical biology | |
| Authors: Max Bonomi and Carlo Camilloni |   |
Details
The ISDB module contains collective variables, functions and biases originally developed for Integrative Structural and Dynamical Biology. They are related but not limited to the interpretation and modelling of experimental data in molecular modelling.
The EMMIVOX functionality implemented in the ISDB modules require the PyTorch C++ APIs (LibTorch) to be linked against PLUMED. Currently, these include:
To activate these functionalities, please follow the installation instructions below.
Installation
To compile PLUMED with LibTorch support, please look at the installation instruction for pytorch. It is highly recommened to install the CUDA version of LibTorch to calculate EMMIVOX efficiently on the GPU.
Once LibTorch has been downloaded and the relevant environment variables are set, one can configure PLUMED with the following options:
> ./configure --enable-libtorch
[!warning] Libtorch APIs are still in beta phase regarding stability, so there might be breaking changes in newer versions. Currently, versions of LibTorch between 1.8.* and 2.0.0 have been tested.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| BAIES | Bayesian refinement of AF models. | ISDB_COLVAR |
| CALIBER | Add a time-dependent, harmonic restraint on one or more variables. | ISDB_BIAS |
| CS2BACKBONE | Calculates the backbone chemical shifts for a protein. | ISDB_COLVAR |
| EMMI | Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. | ISDB_COLVAR |
| EMMIVOX | Bayesian single-structure and ensemble refinement with cryo-EM maps. | ISDB_COLVAR |
| FRET | Calculates the FRET efficiency between a pair of atoms. | ISDB_COLVAR |
| JCOUPLING | Calculates 3J coupling constants for a dihedral angle. | ISDB_COLVAR |
| METAINFERENCE | Calculates the Metainference energy for a set of experimental data. | ISDB_BIAS |
| NOE | Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms | ISDB_COLVAR |
| PCS | Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. | ISDB_COLVAR |
| PRE | Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . | ISDB_COLVAR |
| RDC | Calculates the (Residual) Dipolar Coupling between two atoms. | ISDB_COLVAR |
| RESCALE | Scales the value of an another action, being a Collective Variable or a Bias. | ISDB_BIAS |
| SANS | Calculates SANS intensity. | ISDB_COLVAR |
| SAXS | Calculates SAXS intensity. | ISDB_COLVAR |
| SELECT | Selects an argument based on the value of a SELECTOR. | ISDB_FUNCTION |
| SELECTOR | Defines a variable (of the type double) inside the PLUMED code that can be used and modified by other actions. | ISDB_GENERIC |
| SHADOW | Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. | ISDB_COLVAR |
References
More information about this module is available in the following articles: