AMBER Archive (2008)

Subject: Re: AMBER: Imaging before HBond analysis?

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Fri Apr 11 2008 - 18:09:32 CDT

I'd guess that is what the code you mentioned is doing. Also, I just
wrote a quick awk script to double check the integration, and the
results agree. So, the 3rd column is the occupancy as I described
previously.

Thanks!

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

On 11-Apr-08, at 4:52 PM, Thomas Cheatham III wrote:

>
>> If I can ask a semi-related question: when using the 'radial'
>> command in
>> ptraj, a 3rd column of data is produced. Is this 3rd column the
>> number of
>> neighbours (the occupancy) as determined by the standard equation:
>>
>> n(r) = 4*Pi*rho*int[g(x)*x^2*dx]
>>
>> where the integral is from 0 to r, rho is density, and g(x) is the
>> radial
>> distribution function? Please excuse the pseudo-matlab/latex
>> equation! :-)
>
> I believe this is what I was calculating in the third column;
> easiest way
> to check is to look at the code in transformRadial in actions.c
> which I
> think is doing what is expected (at least with the standard RDF).
>
> - tec3
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