[gmx-users] RE:Data Analysis

lloyd riggs lloyd.riggs at gmx.ch
Wed Oct 5 17:18:09 CEST 2011

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...


Stephan Lloyd Watkins
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