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Re: [lammps-users] WHAM
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Re: [lammps-users] WHAM

From: Giacomo Fiorin <giacomo.fiorin@...24...>
Date: Thu, 17 May 2018 09:46:56 -0400

Hello Teddy, there are examples for multiple methods for a benchmark system with two molecules, which of course you can easily adapt to the two atoms NaCl system:
Umbrella sampling and in general methods based on biased probabilities require WHAM or another unbiasing methods.  Axel mentioned already the widely used implementation by Grossfield, there is also one in the GROMACS analysis tools.

Can you elaborate on what is not working with ABF?  For such a simple system, I find that unlikely unless there are problems in the setup.  In that case, another sampling method is unlikely to give better results.


On Wed, May 16, 2018 at 6:35 PM, teddy baker <edwardbaker86@...24...> wrote:
I am trying to implement the WHAM method to calculate the PMF between two ions in a solution.  I first tried the ABF method but I do not think this is working adequately.  I do not see an implementation of WHAM, could someone suggest how I can use the available tools to most easily implement WHAM, or suggest an alternate colvars method that would work adequately for calculating the PMF for two ions (Na-CL) in water?

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Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD