WHAM implementation and testing

  • Thread starter diegzumillo
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In summary, the individual is seeking resources and references for the WHAM algorithm and its implementation, as they are unsure if their current implementation is accurate. They specifically mention wanting to find a book on numerical methods or a "fool proof system" for understanding the results of density of state and free energy calculations. They suggest searching for about 20 references on the implementation and have found some usable discussions and implementations through a Google search. However, they are unable to access one of the main references due to a paywall.
  • #1
diegzumillo
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TL;DR Summary
Weighted histogram analysis on monte carlo simulations
Hey all
I implemented WHAM to analyze my monte carlo simulations but I am always suspicious that it's not working properly. It gives results that makes sense most of the time but not always. The problem is that all I used is the original paper by Ferrenberg and Swendsen . I have no way of testing if my implementation has bugs.

What I'm asking is if there is a good source on the subject, a book on numerical methods that covers WHAM, maybe. Or maybe just a fool proof system that everyone knows what the results should look like for density of state and free energy based on specific pseudo random gaussians.
 
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  • #2
Suggestion. Want about 20 references on the implementation, then google search: 'WHAM algorithm'
I got several that seem to me to be very usable implementations and discussions. Plus, I cannot see the aps.org paper - paywall. Unless someone else has used this recently the paywall will be an impediment for giving you a good answer. Some folks here no longer have access.
 

1. What is WHAM implementation and testing?

WHAM (Weighted Histogram Analysis Method) implementation and testing is a computational technique used in molecular dynamics simulations to calculate free energy landscapes and kinetics of biomolecular systems. It involves the use of weighted histograms to estimate the probability distributions of various states of the system.

2. How does WHAM implementation and testing work?

WHAM implementation and testing involves collecting data from multiple simulations of the same system under different conditions. The data is then combined using a weighted histogram approach to calculate the free energy landscape and kinetics of the system. This allows for a more accurate and comprehensive understanding of the system's behavior.

3. What are the benefits of using WHAM implementation and testing?

WHAM implementation and testing provide a more accurate and efficient way of calculating free energy landscapes and kinetics compared to traditional methods. It also allows for the analysis of complex biomolecular systems, which may not be possible using other techniques.

4. What are some common challenges when implementing and testing WHAM?

One of the main challenges of WHAM implementation and testing is the selection of appropriate weighting factors. These factors need to be carefully chosen to ensure accurate results. Another challenge is the high computational cost, as multiple simulations are required to obtain reliable data.

5. How can one validate the results obtained from WHAM implementation and testing?

There are several ways to validate the results obtained from WHAM implementation and testing. One approach is to compare the results with experimental data or results from other computational techniques. Additionally, conducting multiple independent simulations and comparing the results can also help validate the findings.

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