VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 03 2014 - 00:58:07 CST

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.