Hi,
On Fri, Feb 1, 2013 at 9:51 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hi Daniel,
>
> I absolutely agree with you, that commands
>
> radial out R1.agr .1 :WAT.O
> radial out R1.agr :WAT.O .1
>
> will provide different results and of course I also
> agree with your explanation why.
If so, then why should these commands:
> #1
> radial WAT_CEN.RDF 0.2 30.0 :WAT :CEN noimage
>
> #2
> radial WAT_gCEN.RDF 0.2 30.0 :CEN :WAT noimage center1
behave any differently? #1 is "What is the probability I see atoms in
residues named WAT a certain distance from atoms in residues named
CEN?". #2 is "What is the probability I see the geometric center of
all atoms in all residues named CEN a certain distance from atoms in
residues named WAT?". These questions are different, and as a result
get different answers. Say I have a system composed of 2 residues, M
(which has 6 atoms) and N (which has 3). If I do something like
'radial X 0.2 30.0 :N :M' I'm calculating these distances:
N0->M0
N0->M1
N0->M2
N0->M3
N0->M4
N0->M5
N1->M0
...
N2->M5
I then normalize appropriately based on the number of atoms in each
mask minus any overlap etc. When you do something like 'radial X 0.2
30.0 :M :N center1', now I'm calculating these distances:
Center = {M0, M1, M2, M3, M4, M5}
Center->N0
Center->N1
Center->N2
This also gets normalized, but it is fundamentally a different
calculation. Hopefully this makes things a little clearer.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Feb 01 2013 - 10:00:02 PST
