[gmx-users] RE:Data Analysis
lloyd.riggs at gmx.ch
Wed Oct 5 17:18:09 CEST 2011
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...
Stephan Lloyd Watkins
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