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:
g(r,R)=(Nc(r,R))/(4*p*d*r^2*dr),
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,
Andres
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?
>
> -tec3.utah.edu
>
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Received on Wed Nov 15 2006 - 06:07:35 PST
