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.
But this obvious fact was not the topic of my original contribution.
So I will repeat the original problem again more in detail and let's please
discuss just this problem.
So I have these two 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
According to the AT12 manual (page 189):
Command #1 should calculate RDF of all WAT atoms with respect to the atoms
in CEN residum/es.
AT12 CITATION:
****************************
"Calculate the radial distribution function (RDF, aka pair correlation
function) of atoms in <mask1> to atoms in <mask2> ..."
****************************
Am I right here ? If not why ?
Command #2 should calculate RDF of all WAT atoms with respect to the
geometric center of all
atoms in CEN residuum/es.
AT12 CITATION:
***************************
"If the center1 keyword is given, the RDF of all atoms in <mask2> to the
geometric center of atoms in <mask1> is calculated."
**************************
Am I right here ? If not why ?
If I am right in both above points, I would also assume that if the CEN
residuum is composed
just of one! single atom and moreover if I have only one! CEN residuum in
my system, the command
#1 should provide identical result as command #2 (i.e.
WAT_gCEN.RDF=WAT_CEN.RDF), simply because in both cases I am doing RDF of
WAT atoms with respect to the very same one point in the space.
If you don't agree please explain why.
But unfortunately at least in my case the commands #1 and #2 do not
provide the identical results.
The results differ here by multiplicative constant "k!=1" so that
WAT_gCEN.RDF=k*WAT_CEN.RDF,
moreover this constant is different for different components of my system
(WAT, Na+, etc.)
Can you explain this behavior ?
Thanks in advance for your final comments,
Best wishes,
Marek
Dne Fri, 01 Feb 2013 17:02:56 +0100 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> Hi,
>
> On Thu, Jan 31, 2013 at 10:27 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>> However, in the second command you are computing the RDF
>>> of the geometric center (i.e. a single point) of the CEN residue(s) to
>>> the atoms in every WAT residue.
>>
>> Here I don't agree with you. My interpretation of the second command is
>> that
>> according to the AT12 manual (page 189) here should be calculated RDF
>> of
>> WAT atoms to the geometric center of the CEN residuum (i.e. to the only
>> one atom which exists in CEN res.)
>
> The command functions exactly the way both you and I describe it. The
> issue here is that I still think the RDF of:
>
> radial out R1.agr .1 :WAT.O
>
> and
>
> radial out R1.agr :WAT.O .1
>
> should not match. My reasoning is this: you can think of the RDF as
> giving you the probability you will see something a certain distance
> from something else, right?. In the first case I'm asking, "What's the
> probability I see atom 1 a certain distance from any water oxygen?".
> Since there are a lot of water oxygens but only 1 atom, the
> probability I see atom 1 from any given water should be pretty low.
> However, in the second case I'm asking, "What's the probability I see
> a water oxygen a certain distance from atom 1". Since there are
> presumably plenty of water residues (and assuming atom 1 is
> solvent-exposed), the probability should be fairly near 1.
>
> Hopefully this helps clear things up. The description of the 'radial'
> command (among others) should definitely be clearer in the manual.
>
> -Dan
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 01 2013 - 09:30:02 PST
