Dear All, I woundered if anyone has scripts/tools or suggestions for analyzing energy changes from extracted run data. Mostly I end up with 20 spread sheet columns for a large system with 2x2 domain proteins, a peptide of 10-20 amino acids and soome small molecules. I've been playing with the data via xmgrace and qtiplot, and using formulas by hand via liturature. I am also breaking things down into simplified energy runs (EQ via NPT 50 ps, then a simple MD for 2-5 picosecounds with the systems components seperated in solvent, and the system components in a complex in solvent. Then extended runs for one or two systems that look nice for different (structural and interaction based) analysis.
Mostly though I just woundered if anyone had scripts (Python, java, C++, etc...) for manipulation the extracted energy data and producing an output column for totals, or a summed single number output for varied energy components. Mostly I found the Gromacs normal data manipulation (g_lie) works well with small molecules for a simple quick EQd run, but not for large proteins, etc... Sincerely, Stephan Lloyd Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
