AMBER Archive (2005)

Subject: Re: AMBER: Question about radial command in ptraj

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Mar 14 2005 - 15:09:08 CST

It seems to me that if the interval is, say, .1 Angstrom,
the only reasons for a not-smooth curve would be lack of
data points or bug in the code. If the former, I wonder
if Insight performs some smoothing on the curve? Or
possibly you are not specifying what you think to ptraj?
I would post ptraj input if you haven't already.

See the manual for how to do it in carnal. The plan is
to discontinue it in future releases since ptraj does
pretty much the same thing and has more active support.
(I have offered to give advice to anyone who wants to
maintain or extend carnal, but am no longer active in
this field aside from offering advice.)

Bill

> The problem with specifying more intervals in ptraj simply has more
> increments, while the shape of the curve is still jagged and has sharp
> corners rather than a smooth function.
> In the past I had used InsightII to get the g(r), but I do not have
> access to it anymore. In InsightII the g(r) for the same molecule was
> smooth, while in ptraj it comes out jagged. That is ultimately why I am
> asking the question, I know that the g(r) of this molecule can look
> smooth, but am not sure if or how I can get it from Amber/ptraj.
> If Carnal can do this, how would I get a g(r) from carnal?
>
> Best Regards,
>
> Armin
>
> ==============Original message text===============
> On Mon, 14 Mar 2005 14:48:17 EST Bill Ross wrote:
>
> Carnal also does radial distributions, and you can specify
> the radial increments. Possibly ptraj allows this as well?
>
> Bill
>
>
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