Free WHAM Functions

This document explains the functions in eSBMTools that were used in this example.

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→ 1 module from eSBMTools was imported into freeWHAM.py:

            -FreeWHAM.py

→ The function

    getTQE(os.getcwd() + '/simdata/', 'pdb_code')

is used to get a list of the simulation temperatures, the Q values and the energy values for the
simulation data.

This is a function of FreeWHAM.py

→ After this, we define the minimum and maximum temperatures over which the simulation was run and the
time step of the simulation (which can be found in the .mdp file used for the simulation). For this
example, we ran the simulation from 98 K to 118 K with a timestep of 0.01.

→ Next we use the function

    getFreeEnergy(tList, qList, eList, tMin, tMax, tStep)

where,  (tlist, qlist, elist) obtained from getTQE()
        (tMin, tMax, tStep) specified earlier

to get the following information from the simulation data:

(1) -free energy landscape as function of temperature and Q
(2) -heat capacity as function of temperature
(3) -maximal and minimal Q value in trajectories

→ Now that we have all the information necessary for freeWHAM, we plot the graph using the following
function:

    plotFree(freeArray, tArray, cv, qmin, qmax)

  where,    freeArray and tArray from................(1)
  and       cv from..................................(2)
  and       qmin and qmax from.......................(3)

→ The above three functions are a part of the FreeWHAM module.

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Cheers!