Hello Daniel,
first of all thanks a lot for your prompt answer !
Please check my comments.
Dne Fri, 01 Feb 2013 05:37:30 +0100 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> Hi,
>
> On Thu, Jan 31, 2013 at 4:47 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>> these two commands
>>
>> radial WAT_CEN.RDF 0.2 30.0 :WAT :CEN noimage
>> radial WAT_gCEN.RDF 0.2 30.0 :CEN :WAT noimage
>> center1
>>
>> should provide identical results (i.e. WAT_CEN.RDF=WAT_gCEN.RDF ),
>> instead
>
> I don't think that's correct. In the first command you are computing
> the RDF of the atoms in every WAT residue to the atoms in CEN
> residue(s).
That's right ! (I just amend here that 1 atom. CEN res. is only one such
res. in my system.)
It pretty agrees also with the AT12 manual where is written:
****************************
"Calculate the radial distribution function (RDF, aka pair correlation
function) of atoms in <mask1> to atoms in <mask2> ..."
****************************
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.) Here is the relevant citation from the
manual:
***************************
"If the center1 keyword is given, the RDF of all atoms in <mask2> to the
geometric center of atoms in <mask1> is calculated."
**************************
If I am not right here, please write the right command which should
calculate RDF of
WAT atoms to the geometric center of CEN res. please.
Obviously I already tried the reverse possibility:
radial WAT_gCEN.RDF 0.2 30.0 :WAT :CEN noimage center1
This doesn't work, it is much worse than in case of my original command
(which is in my opinion in
agreement with AT12 manual) because now the shape of the RDF profile
(WAT_gCEN.RDF) is quite different from WAT_CEN.RDF. I mean that the
difference is no not just by multiplicative constant, (as in original
case) the shape is simply quite different.
So please put more light here ...
Best wishes,
Marek
Also, note that the default density
> value is 0.033456 molecules/Ang^3 which corresponds to a density of
> water approximately equal to 1.0 g/mL; if you're calculating something
> different you need to adjust (or just use the 'volume' keyword) if
> your system has periodic box info. For example, when you're
> calculating :CEN to :WAT you're calculating 3 distances to each water
> (O and 2 Hs) instead of 1 so the density value would need to be
> adjusted appropriately with the 'density <density>' keyword.
>
> Hope this is helpful,
>
> -Dan
>
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Received on Thu Jan 31 2013 - 22:00:03 PST
