VMD-L Mailing List

From: Nifeng Guo hui (nifenggaohui_at_gmail.com)
Date: Tue Nov 04 2014 - 13:07:26 CST

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
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.

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.
>