[gmx-users] Computing work from pulling simulations

[Leandro Bortot]

Have you compared the results of your calculation using the forces at
different intervals? e.g. every 1, 10, 50, 100 steps ?

As long as you use a not-so-large interval the result should be the same
within statistical error.

Cheers,
Leandro


On Mon, Jun 19, 2017 at 7:19 PM, Lutz Maibaum <lutz.maibaum at gmail.com>
wrote:

> I am using “umbrella pulling” to simulate the dissociation of two
> molecules. I would like to calculate the work W(t) that the harmonic trap
> has performed on my system up to timestep t, which can be calculated as
>
> W(t) = sum_{i=0}^t F_i * v * dt
>
> where F_i is the biasing force at timestep i, v is the pulling velocity,
> and dt is the timestep. The latter two I set in the .mdp file, and the
> force is written out by Gromacs to the  pull_pullf.xvg file.
>
> This works very well. However, computing the work using the equation above
> requires me to save the forces to a file _every single timestep_, which
> becomes unfeasible for longer simulations. Does Gromacs keep track of the
> cumulative work performed by the umbrella potential, and does it save that
> value somewhere? I couldn’t find it in the .edr or log files (I am using
> Gromacs 5.1.4).
>
> Best,
>
> Lutz
>
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