AMBER Archive (2008)

Subject: Re: AMBER: Imaging before HBond analysis?

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Fri Apr 11 2008 - 17:41:51 CDT

Dear Thomas,

Thanks for the speedy reply! I'll keep this in mind when using HBond.

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! :-)

Thanks!

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

On 11-Apr-08, at 4:24 PM, Thomas Cheatham III wrote:

>
>> I am wondering if the HBond function in ptraj (Amber version 9)
>> implicitly
>> handles PBC imaging considerations, or if an image command must be
>> issued
>> before the hbond command? The manual doesn't seem to state one or
>> the other
>> is the case.
>
> It looks like imaging is disabled in the distance calculations of
> hbond so
> imaging is likely necessary prior to the hbond command. I will fix
> this
> to match default behavior (of implicitly imaging) [which will slow
> down
> the command significantly unless "noimage" is specified] in an
> upcoming
> AmberTools release and also will update the manual...
>
> For now, image prior to doing the hbond command...
>
> -- tec3
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