Free WHAM Functions modified by Ramneek

Ramneek — Wed, 26 Mar 2014 15:55:14 -0000

--- v1
+++ v2
@@ -10,15 +10,14 @@

        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.
+  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.
+→ 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

@@ -33,8 +32,8 @@
    (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:
+→ Now that we have all the information necessary for freeWHAM, we plot the graph using the following
+  function:

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

Free WHAM Functions modified by Ramneek

Ramneek — Wed, 19 Mar 2014 15:34:06 -0000

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

→ 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.

Cheers!

Recent changes to Free WHAM Functions

Free WHAM Functions modified by Ramneek

Free WHAM Functions modified by Ramneek