[gmx-users] Procedure About Free Energy calculation

PeiQuan Chen gromacs at 163.com
Thu Jun 12 09:02:01 CEST 2003

Dear gmx-users:
    Recently I have read some of the literature which discussed the free energy perturbation. I begin to grasp some of the ideas about this computational techique.
    I know that there are three methods that have been proposed for calculating free energy diffeneces: statistical perturbation(SP), thermodynamic integration(TI) and slow growth(SG). From the gromacs manual, I think that gromacs pakages can implement all of the three methods in free energy calculating. But I don't understand enough how to use the gromacs pakages to do a free energy calucualting.
  For example, If I want to calculate the free energy between Cl-(state A) and Br-(state B) in water. Can anybody give me some hints on how to perform these calculations.

  As I have got help from Alessandra Villa, I know how to perform TI calculation.


1) run a number of indipendent simulations (i.e. 20) at different values
   of lambda.
   Lambda must have a value between 0 (state A) and 1 (state B).

2) take the average values of dV/dl for each simulation using g_energy or g_analize.

3) thus, for each lambda point from 0 to 1, you will have an values of
   dV/dl. Integrate the curve using xmgr (with the trapezoid method) 

   The value that you get is DG  passing from state A to state B      

   But I can't understand how to use statistical perturbation and slow growth method to calculate free energy. Does anybody
can give me procedures like above how to calculate free energy using slow growth method and statistical perturbation.

   Thank you for any help!

Sincerely yours
PeiQuan Chen
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	

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