VMD-L Mailing List

From: Ern Seang Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Tue Aug 18 2015 - 20:38:57 CDT

Hi VMD users,

I have listed following questions about extracting data from NAMD log file.

1. I have run a simulation and I need to calculate the viscosity of the equilibrated system by using Green-Kubo relation. For the viscosity calculation, I need to the values of stress tensor (pressure in 3x3 matrix), temperature and volume, which are available in the NAMD log file, but I do not know how to extract those values out into a spreadsheet.

2. Is there any way for me to export the graph as displayed in multiplot?

3. Is there any Tcl script available for viscosity calculation (using eg. Green-Kubo relations) in VMD?

Thank you.

Ernest

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