[gmx-users] free energy landscape

[Justin Lemkul]

On 11/28/13 7:20 AM, aixintiankong wrote:
> Dear, i want to make a free energy landscape with respect to Rg and RMSD.
> First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate.
> And the i merge the rmsd value and Rg value into one file with two column,
> then i use the g_sham command to got the free energy landscapes. does it
> right or not? i have seen dihedral PCA from your website (

Yes, that's correct.

> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=landscape),
> should i use the g_covar and g_anaeig commands to get the free energy
> landscape with respect to Rg and RMSD? if yes, please tell how to do it ,
> thank you very much!
>

g_covar and g_anaeig are necessary in that case to extract the data of interest; 
those programs have no bearing on what you are doing.  The process is identical 
though - generate a text file of the two variables of interest (for 
g_covar/g_anaeig, the columns are eigenvalues) and then plot with g_sham.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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