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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