VMD-L Mailing List

From: Paymon Pirzadeh (ppirzade_at_ucalgary.ca)
Date: Mon Feb 13 2012 - 21:43:54 CST

Dear Axel,
You pointed to an important issue about the selection string.
In my case, my first selection string was "resid 10 11 14 15 ..." and my
second selection string was "name OW and within 10 of resid 10 11 14
15 ...". Is my selection a "bad" one in your opinion? How can I stay on
the safe side?
Sorry for mass of questions, but this RDF turns out to be very iportant
to my work, and I want to get it done at least with some solid grounds.

Paymon

On Mon, 2012-02-13 at 22:32 -0500, Axel Kohlmeyer wrote:
> paymon,
>
> please always copy the list on any responses.
>
> On Mon, Feb 13, 2012 at 10:06 PM, Paymon Pirzadeh <ppirzade_at_ucalgary.ca> wrote:
> > Hi Axel,
> > Thanks for your respond. I recalculate the rdfs with pbc. Can one easily
> > compare such profiles among different proteins? But then can one report
>
> depends. in general, no.
>
> the normalization is based on some arbitrarily chosen
> density. in this case the density of bulk water at 300 K
>
> the information that is independent from the normalization
> are the peak positions and the running integral, i.e. how
> many atoms are "under" the graph up to a given peak.
> but even there, the exact choice of the selection string
> is important and "bad" choice can make results difficult
> or impossible to compare.
>
> this is a non-trivial issue.
>
> > and publish such profile?
>
> for as long as you don't fully understand how and
> why the normalization is arbitrary, i recommend
> against publishing any of those results.
>
> axel.
>
> >
> > Paymon
> >
> >
>