AMBER Archive (2006)

Subject: AMBER: Ptraj: radial distribution and correlation coefficient

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Tue Nov 14 2006 - 12:10:39 CST

Dear Amber users,
I am using ptraj to calculate some radial pair distributions between
specified solute atoms and water molecules. At the end of the run ptraj
also prints out a "segmentation fault." However, the output files look
fine (ie correct number of frames).
Secondly, the output files have three columns. Below are the head and tail
of one of the rpd files:

   0.050 0.000 0.000
   0.150 0.000 0.000
   0.250 0.000 0.000
   0.350 0.000 0.000
   .......................
   9.650 0.952 114.140
   9.750 0.961 117.983
   9.850 0.956 121.880
   9.950 0.962 125.887

It seems the second column represents rpd values. Would be glad to know
what the third column stands for?

I am also calculating correlation coefficients from the same trajectory.
Here is my input file:

trajin md.crd
vector vec :1-3 dipole
analyze correlationcoefficient {vec | ALL}
go

But I keep getting this error message:
ptraj(), analyzeCorrelationCoefficient: cannot find a match in the
scalarStack for name ({vec), returning
Does anyone know what I am not doing correctly?
I am using the ptraj version that comes with the AMBER8 package.
Thanks,
austin-
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