[gmx-users] For free energy landscape!

dxli75 dxli75 at 126.com
Wed Aug 19 17:23:30 CEST 2009

Dear All,


    I have make a free energy landscape by using the data of RMSD and H-bond number of main chain of a protein according to the following method. I am not sure if the method does work. If not, Could you give me some advises? Thank you!

PS: Method

   1. Obtained the RMSD and the number of H-bond of mainchain of the protein by using g_rms and g_hbond commonds;

   2. Copy above two groups of values (RMSD and H-bond number) into Origin Software. first column is values of H-bond number, second column is RMSD;

3. Statistics > Descriptive Statistics > 2D Frequency Count in Origin, and obtained a matrix named as"TwoD FreqCounts";

4. Convert the above matrix into worksheet with type of xyz, and  got the values in the third column (frequency counts of RMSD and H-bond number);

5. Calculate the frequency count into normalized possibility;

6. Select the maximal or minimal possibility as control value.

   If  you select the maximal possibility (Pmax) as control value, the ΔG = Gx - Gmax = -kBTln(Px/Pmax) > 0;

   If  you select the minimal possibility (Pmin) as control value, the ΔG = Gx - Gmin = -kBTln(Px/Pmin) < 0;

Calculate all the values of (Px/Pmax) or (Px/Pmin) as the new third column. Here I choose Pmin (frequency count = 1) as control value, and get negative values of free energies;   

7. Convert the values in above three columns into a new matrix by using the method of XYZ Gridding. 

8. According to the above new matrix, plot the final free energy landscape.    



Dx Li
Mechanic Engineering Department
College of Engineering and Computing
University of South Carolina
300, Main Street, 29208
Columbia, SC
Tel: 803-9316307(M); 803-7771299(O)
E-mail:Daixi at cec.sc.edu
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