[gmx-users] For free energy landscape!

[David van der Spoel]

dxli75 wrote:
> 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;

Then you can try using g_sham as well.

> 
>    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 = G_x - G_max = -k_B Tln(Px/Pmax) > 0;
> 
>    If  you select the minimal possibility (Pmin) as control value, the 
> ΔG = G_x - G_min = -k_B Tln(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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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