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 -- ================================================== 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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.