From: Tim Lo (
Date: Tue Nov 04 2014 - 20:48:32 CST

Hi Peng,

You may feel uncomfortable about Axel's comments but what he says is for
your benefit. It prevents you from just superficially *knowing* the
answer without thoroughly *understanding* the answer. For some
fundamental conceptual questions, it may be too tedious and impractical
to answer them in full detail in this mailing list. If you can find the
answer yourself, you can understand the answer in depth and you will be
able to gear up to tackle similar problems in the future. Actually,
there are often some references in the webpage of each VMD plugin. For
the g(r) plugin, see Axel have provided
some useful references there, including the calculation principles
implemented in the plugin.


On 2014/11/5 上午 04:29, Axel Kohlmeyer wrote:
> On Tue, Nov 4, 2014 at 2:07 PM, Nifeng Guo hui <> wrote:
>> Hi Axel,
>> Your response always answer the questions that I did not expect. For
>> example, here I have no interest to doubt there is a problem with g(r)
>> plugin. Second, I did not learn too much from your implication. So, please
> there is good questions and bad questions. you cannot expect a good
> answer to a bad question. full stop.
>> explicitly answer people's question instead of wording them. Though I still
>> thanks for this thread which let me know it is very important to select how
>> precisely the two objects when study RDF. Thanks.
> if you don't understand a g(r) - and from your questions and responses
> it is obvious that you don't - there is little point in discussing
> questions like you are asking. in fact, i content that if you'd have
> the proper understanding, you don't need to ask those questions. all i
> could do is summarize and repeat the stuff from the relevant text
> books. there is no simple "this is right" or "this is wrong" answer.
> it all depends on what you want to learn from the g(r) and that
> requires that you understand in full what it means. it is not the task
> of this mailing list to make up for your lack of experience in
> statistical mechanics. sorry, you *have* to sit down and learn this
> stuff.
> axel.
>> Peng
>> 2014-11-03 0:58 GMT-06:00 Axel Kohlmeyer <>:
>>> On Sun, Nov 2, 2014 at 11:19 PM, Nifeng Guo hui <>
>>> 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 <>:
>>>>> 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
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.