VMD-L Mailing List

From: joy tehrani (joy_tehrani_at_yahoo.com)
Date: Thu Mar 06 2008 - 06:45:35 CST

Dear All
   
  I am interested to use the RMSD trajectory tool and when get the RMSD for each frame and save this information as a file.Then I Like to know ,how I should calculate the diffusion coeffient for this file and how I can have a plot of time and diffusion coefficient in Excel.
  ps.For ex:I have 40 frames and I ran the simulations for 10000 fs in namd.when I want plot the diffusion coefficient with time in a plot ,what should I put in the time columns ,before making this chart.
   
  Thanks A million
   
  Joy

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