AMBER Archive (2003)

Subject: diffusion coefficients

From: yuan bo (yuanbous_at_yahoo.com)
Date: Sun Apr 13 2003 - 21:34:25 CDT

Dear Amber users
I am simulating protein in mixed solents and saved
trajectory in every 0.2ps for analysis. now I want to
calculate diffusion coefficients of solvent for one
100ps trajectory ( 500=100/0.2 sets data, using Ptraj
program in Amber 6. Manual define diffusion as
follows:
  diffusion mask time_per_frame [ average ] [
filenameroot ]
The time_per_frame sepicifies time between frams in
ps. I use " diffusion :WAT 4 average filename" command
to calculate.In figure from filename_r.xmgr, X axis
scale is displayed to be 0-2000. I am a little
confused what meaning is 2000, 2000ps? because x
axis'units is picosecond as mentioned in manual. but I
only calculate 100 ps trajectory. why X axis change
2000(500 sets *4 ps=2000?)? it'unit is still
picosecond? Maybe I don't understand what meaning is
time-per-frame?
  Diffusion coefficent can be obtained from the slope
of the line. But I would like to calculate diffusion
coefficent of several intersting solvent molecules.
Howere there is no straight line in filename_r.xmgr
figure but one curve with big fluctuation when I use
method above to calculate. How should I obtain
diffusion coefficient from the such filename_r.xmgr?
 Anybody could help me to understand the two problem?
Thanks a lot?
yb

  
  

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