Hi,
I would like to use constraint force pull code to calculate the free energy
of association of two peptide using the distance between center of mass of two
peptides as reaction coordinate. I am planning to use gromacs 4.
Here I have some queries:
1. Since I will constraint method, I guess, I do not have to use any
force-constant ( unlike umbrella sampling) . If that is correct, do I need to
specify a pulling rate ? If so, what will be a typically appropriate range of
value to start with ?
2. In umbrella sampling technique, we check the overlap of position histogram
of two consecutive windows to check the convergence . Here , using constraint
force technique, what should I check for convergence. Is that the force ?
3. Once I get time series of force for all windows, how should I unbias the
effect of constraint and what formula I should use to integrate the force? Is
that integration implemented in gromacs ?
Thanks
Sanku
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