Hi Daniel,
the problem is evidently in our different interpretation of command
#2
radial WAT_gCEN.RDF 0.2 30.0 :CEN :WAT noimage center1
YOUR INTERPRETATION IS:
**************************************************************************
#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?".
****************************************************************************
MY INTERPRETATION IS:
*************************************************************************
#2 is related to the probability I see the WAT atoms in a certain distance
"r"
form the geometric center of all atoms in CEN residuum/es.
In another words, as I already wrote, in my opinion (and also according to
the AT12 manual page 189) Command #2 should calculate RDF of all WAT atoms
with respect to the geometric center of all atoms in CEN residuum/es.
*************************************************************************
AT12 CITATION IS:
***************************
"If the center1 keyword is given, the RDF of all atoms in <mask2> to the
geometric center of atoms in <mask1> is calculated."
**************************
So my interpretation is based on definition in AT12 manual. What is the
base of your interpretation ?
If the above command is really not! in agreement with my! interpretation,
could you please
simply write the proper command which is! in agreement with my!
interpretation.
Thanks a lot in advance !
Best wishes,
Marek
----------------------------------------------
Dne Fri, 01 Feb 2013 18:41:03 +0100 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> 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
>
--
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Received on Fri Feb 01 2013 - 10:30:03 PST
