From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 03 2014 - 15:49:48 CST

On Mon, Nov 3, 2014 at 4:29 PM, Nifeng Guo hui <nifenggaohui_at_gmail.com> wrote:
> Hello, Axel and Tim
>
> I analyze RDF in production run of 10 ns. (After energy minimization and
> NVT, NPT Equilibration simulation.) In my understanding of RDF, after
> certain distance from the reference point, the particles will distribute
> evenly which means water molecules are not attracted or repelled by the
> protein molecule. Thus, the water density will appear as a horizontal line.
> However, it's hard to explain that RDF increases to 28 anstrom and suddenly
> becomes zero.

it suddenly becomes zero, because you run out of data. under
consideration of minimum image conventions you usually are only able
to compute the g(r) up to half the shortest box length. the g(r)
calculation in VMD uses a smarter normalization function that can go
beyond that, with the maximum being half the length of the diagonal
through the box (with limited statistical accuracy, due to the
shrinking normalization volume).

> Now, I change the code in "Section 2" as "name OH". The plot seems like
> understandable. So does this mean the code for "water" in "Section 2" is
> incorrect? I attach the new plot. Please take a look at it. Thanks.

your question has nothing to do with the g(r) calculation but with
VMD's atom selection language. the g(r) plugin will compute what you
ask it to compute. whether you select the right group(s) of atoms for
your purpose is something that you have to validate independently.
when using macros like "water", you have to make certain, that your
input conforms to the underlying heuristics. this is not the g(r)'s
plugin's job, but yours. from the point of the plugin, there is no
"right" or "wrong". it just uses your input. please revert to the VMD
user's guide for details.

axel.

>
> Peng
>
> 2014-11-03 0:58 GMT-06:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
>
>> On Sun, Nov 2, 2014 at 11:19 PM, Nifeng Guo hui <nifenggaohui_at_gmail.com>
>> wrote:
>> > Hi Tim,
>> > Thanks for the explanation. Now I follow your instruction and plot it
>> > again.
>> > It still does not make sense. I use period boundary condition to
>> > simulate in
>>
>> well, the problem is very likely not with the g(r) plugin but with
>> your expectations. you most certainly don't have a homogeneous
>> monoatomic fluid as your system, which will lead to the graphs more
>> commonly seen as examples for a g(r). please review the definition of
>> the g(r) (i.e. what the graph means, not what it typically looks like)
>> and compare it to the structure you are feeding into VMD. i am very
>> confident that what you see as a graph is correct. it would be
>> consistent with a two component system that is mostly separated.
>>
>> > a cubic box with dimension 50. The molecule size is
>> > cellBasisVector1 48.12900161743164 0 0
>> > cellBasisVector2 0 42.979000091552734 0
>> > cellBasisVector3 0 0 43.9109992980957
>> > cellOrigin 0.5063787698745728 1.1608952283859253 0.11323882639408112.
>> > Please find the picture in the attachment. Thanks.
>> > Peng
>> >
>> > 2014-11-02 19:19 GMT-06:00 Tim Lo <timlo_at_hku.hk>:
>> >
>> >> Hi Peng,
>> >>
>> >> By looking at the r-axis, the graph just displays g(r) for the range of
>> >> [0, 10]. You should increase "max r" to your desired value, but not
>> >> just use
>> >> the default value of 10.0.
>> >>
>> >> Tim
>> >>
>> >>
>> >> On 2014/11/3 上午 06:01, Nifeng Guo hui wrote:
>> >>>
>> >>> Dear VMD users,
>> >>> We perform one simulation with one protein immersed in water. Now, we
>> >>> want to analyze the water distribution around this molecule after
>> >>> finishing
>> >>> production run. The g(r) GUI Plugin, Version 1.3 was applied to
>> >>> calculate
>> >>> its function. After I input PSF and DCD files, I put "residue 1 to 36"
>> >>> in
>> >>> Section 1 and "water" in Section 2. (This protein is composed of 36
>> >>> amino
>> >>> acids. ) I also tried "protein" for Selection 1. Next, Frames are "0"
>> >>> in
>> >>> First and "19999" in Last. Then before using compute g(r), I select
>> >>> Use PBC,
>> >>> Display g(r), and Display int(g(r)). However, the result does not
>> >>> reach our
>> >>> predictions. The RDF and Coordination number are both increasing
>> >>> exponentially as r increase. In our prediction, it supposes to become
>> >>> constant. Could you help me find what cause this? Plese also take a
>> >>> look at
>> >>> the plot in the attachment. Thanks.
>> >>> Peng
>> >>>
>> >>>
>> >>>
>> >>
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.