[gmx-users] Re:Data Analysis

[lloyd riggs]

Dear All,

Is there a way to extract the pull force (and not the total force or energy) 
for a specified group (indexed) or center of mass, rather than just the total 
pullf over a run?  I wanted to break up the pullf into varied sub 
contributions, however as it is applied to the center of mass of the pull 
group, I do not know if it is possible.  I am just trying to sort out easier 
Vs. More complicated means of doing the same thing as there are several methods 
for achieving the end result I wanted (output plots).

Any suggestions are appriciated as well.

Sincerely,

Stephan Lloyd Watkins
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[gmx-users] RE:Data Analysis

[lloyd riggs]

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
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