Gromacs
2021beta2UNCHECKED

AWH calculates the free energy along an order parameter of the system. Free energy barriers are overcome by adaptively tuning a bias potential along the order parameter such that the biased distribution along the parameter converges toward a chosen target distribution. The fundamental equation governing the tuning is: log(target) = bias  free energy, where the bias and free energy are initially unknown. Typically the target distribution is simply chosen uniform, such that the bias completely flattens the free energy landscape.
The module implements AWH for the case when the order parameter corresponds to a reaction coordinate, here referred to as coordinate for short, i.e. a function of the system configuration. The bias is coupled to the system by a bias potential: either in the form of an harmonic ("umbrella") potential MonteCarlo (MC) "jumping" around the current coordinate value, or as a smooth convolution of the umbrellas.
The AWH module is organizes as follows: The Awh class is the interface between the outside and inside of the module. The Awh class contains one or more BiasCoupledToSystem objects. The BiasCoupledToSystem class takes care of the reaction coordinate input and force output for the single Bias object it containts. The Bias class is a container and wrapper for a object BiasState + helpers. All computation takes place in the BiasState object and its subclasses. The Bias class also contains a BiasWriter object that takes care of i/o.
The basic use of Awh in mdrun consists of 2 method calls: Call the constructor Awh() after the pull module has been initialized. Call applyBiasForcesAndUpdateBias() at every MD step after the pull potential calculation function has been called.
In grompp the pull potential provider should be registered using registerAwhWithPull() so grompp can check for unregistered potentials.
The main tasks of AWH are:
AWH currently relies on the pull code for the first task. Pull provides AWH with updated coordinate values and distributes the bias force that AWH calculates to the atoms making up the coordinate. This also means that there are some order dependencies where pull functions need to be called before AWH functions (see below).
The implementation is quite general. There can be multiple independent AWH biases coupled to the system simultaneously. This makes sense if the system is made up of several fairly independent parts, like monomers in a protein. Each bias acts on exactly one, possibly multidimensional, coordinate. Each coordinate dimension maps to exactly one pull coordinate. Thus, an ndimensional biased coordinate is defined by a set of n pull coordinates. Periodicity is taken care of for coordinate dimensions that require it (dihedral angles). For increased parallelism, there is the option of having multiple communicating simulations sharing all samples. All simulations would then share a single bias and free energy estimate. Alternatively, one may partition the sampling domain into smaller subdomains with some overlap and have multiple independent simulations sample each subdomain.
Note that internally the AWH module keep tracks of free energies in units of the thermal energy kT. This is because we mostly deal with free energies in the form of log(probability) and using any other unit would be bug prone. All energy type variables are explicitly documented to be in units of kT. Also the checkpoint and energy file data is in units of kT. The analysis tool will by default convert energies to kJ/mol, but there is also a kT option.