Dear Amber Users,
I am interested in calculating velocity-autocorrelation-functions and radial distribution-functions of different solvents. I used Ptraj to calculate this functions, but there were some problems. What is exactly calculated by the command radial ?
When I calculated the radial distribution-function by the command radial (radial radtoluol.out 0.05 8.0 :100 ) I had a very low resolution of the function, when I increased the number of bins by spacing always g(r) increased. Is there any possibility to normalize the function ?
Is the radial-distribution-function calculated by the center of mass ? The distance of the first layer is always too short in my case, what are the units of the result ?
Many thanks for your help
Peter Trodler
Institute of Technical Biochemistry
University of Stuttgart
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Received on Tue Sep 09 2003 - 10:53:06 PDT
