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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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