AMBER Archive (2006)

Subject: Re: AMBER: Ptraj: radial distribution and correlation coefficient

From: Andres Palencia (
Date: Tue Nov 14 2006 - 14:13:39 CST

Hi everybody,

according with the mails about the calculation of radial function, It
would be very nice for me to know if the rdf used in Amber8 corresponds
with the equation:
where Nc is the average coordination number between r and dr around
atomic site R at time t, p is the number pi and d is the density of
water oxygen around atomic site R.
Does correspond the second column in the outputfile "standard*xmgr"
with g(r,R)?, it means that it is possible to calculate the value of
Nc?, and which value of density should we use to substitute in the
previous equation? I guess that the value of "d" in the previous
equation does not correspond with the standard value of 1 g/ml for water.

Thanks in advance,


Thomas Cheatham wrote:
>> trajin md.crd
>> vector vec :1-3 dipole
>> analyze correlationcoefficient vec
> ...
>> ptraj(), analyzeCorrelationCoefficient: cannot find a match in the
>> scalarStack for name (vec), returning
> Hmmn, I look into that...
>> trajin md.crd
>> #vector vec :1-3 dipole
>> analyze correlationcoefficient ALL
>> go
>> Returns this error message:
>> ptraj(), analyzeCorrelationCoefficient: missing the second name on
>> scalarStack to process... Returning.
> Yes, I e-mailed too quickly; you need to specify two scalar variables.
> Also, the "vector" is not a scalar so the correlationcoefficient command
> is not what you want.
> What do you want to do? Perhaps see the "correlation" command?
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