AMBER Archive (2003)

Subject: AMBER: radial distribution-function by Ptraj

From: Petrodler_at_aol.com
Date: Tue Sep 09 2003 - 04:15:10 CDT

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu