Calculations of thermodynamic data and other properties rely on proper sampling of the configurational space. However, the presence of energy barriers can prevent certain configurations from being sampled properly or even sampled at all. Umbrella sampling is a simulation technique that helps to overcome those barriers and improve sampling by applying a bias along a specified collective variable. The bias takes the form of a harmonic potential and is typically constant throughout a simulation. Usually, a series of umbrella-sampled simulations are performed and analyzed together using the weighted histogram analysis method (WHAM).
The functional form of the artificial bias is
where \(k\) is the spring constant, \(s\) is the current value of the collective variable and \(s_0\) is the desired value of the collective variable. The success of the umbrella sampling method depends on the correct choice of \(k\) and \(s_0\) for the different simulations. Suitable values of \(k\) and \(s_0\) depend on the distances between adjacent umbrellas, and the gradient of the free energy surface at \(s_0\).
For more information about the umbrella sampling method, the interested reader is referred to Ref. .
Options & Parameters¶
The following parameters need to be set under “method” in the JSON input file:
"type" : "Umbrella"
The following options are available for Umbrella Sampling:
- centers (required)
- Array of target values for each CV. This can either be an array of numbers, or an array of an array of numbers, for multiple walkers. If only a single array is defined, it is used across all walkers.
- ksprings (required)
- Array of spring constants for each CV. This can either be an array of numbers, or an array of an array of numbers, for multiple walkers. If only a single array is defined, it is used across all walkers.
- output_file (required)
- Output file name for umbrella sampling data. This can be a string or an array of strings for multiple walkers.
- output_frequency (optional)
- Frequency of writing to output file (default: 1)
- append (optional)
- Boolean value which will cause umbrella sampling to either append to an existing file or override it entirely.
The umbrella sampling method can also be run with time dependent centers. This is equivalent to the “steered MD” method. To do so, omit “centers” and use the following options instead:
- centers0 (required)
- Array of initial target values for each CV. This can either be an array of numbers, or an array of an array of numbers, for multiple walkers. If only a single array is defined, it is used across all walkers.
- centers1 (required)
- Array of final target values for each CV. This can either be an array of numbers, or an array of an array of numbers, for multiple walkers. If only a single array is defined, it is used across all walkers.
- timesteps (required)
- The number of timesteps over which to scale the umbrella centers
By setting the above options, the umbrella method will linearly interpolate between centers0 and centers1 in timesteps iterations.
This tutorial will go through running Umbrella Sampling on an atomistic model of butane using LAMMPS as the MD engine. Umbrella sampling will be performed on the torsional CV of the butane C atoms.
The butane implementation in LAMMPS requires several modules to be added before being linked to SSAGES.
To do this, return to your LAMMPS
src directory and issue the following commands
make yes-MOLECULE make yes-KSPACE
which add the
KSPACE LAMMPS packages. Additional information about building LAMMPS with optional packages can be found in the LAMMPS documentation.
The files for running this example can
be found in
Examples/User/Umbrella and consist of the following files:
- LAMMPS input file
- LAMMPS data file describing butane molecule.
- Template JSON input containing information for one Umbrella Sampling simulation.
- Python script for creating Umbrella.json input file. The total number of simulations and the ‘centers’ values are controlled in this file.
Once in the directory, the appropriate .json file needs to be generated. A .json file is already in the directory,
Template_Input.json, which contains the CV information and specifies the LAMMPS input files to be used. Using
Umbrella.json contains the information from
Template_Input.json duplicated 12
times with varying values of
centers. These values correspond to the target values of the torsional CV.
To run SSAGES issue the command:
mpiexec -np 12 /path/to/SSAGES/build/.ssages Umbrella.json
This will run 12 different umbrella sampling simulations simultaneously. Ideally, this example will be run in computing environment where each process can run on a different processor. Though the example will still work if run on a users local desktop or laptop machine, the runtime of the code will be very large.
During the simulation 12 different output files will be generated, each containing the iteration, target value of the corresponding ‘center’ CV, and the value of the CV at the iteration number.
These output files can then be used to construct a complete free energy surface using the WHAM algorithm . Though SSAGES does not currently contain its own implementation of WHAM, there are many implementations available, such as that provided by the Grossfield Lab .
|||Kästner, J. (2011). Umbrella sampling. Wiley Interdiscip Rev Comput Mol Sci, 1(6), 932–942.|
|||Kumar, S., Rosenberg, J., & Bouzida, D. (1992). The weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method. Journal of Computational Chemistry, 13(8), 1011–1021.|
|||Grossfield, A. WHAM: the weighted histogram analysis method. http://membrane.urmc.rochester.edu/content/wham|