## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Tue Nov 04 2014 - 11:39:49 CST

**Next message:**Nifeng Guo hui: "Re: Fwd: namd-l: Why RDF increases as r increase instead of constant"**Previous message:**Nifeng Guo hui: "Re: Fwd: namd-l: Why RDF increases as r increase instead of constant"**In reply to:**Nifeng Guo hui: "Re: Fwd: namd-l: Why RDF increases as r increase instead of constant"**Next in thread:**Nifeng Guo hui: "Re: Fwd: namd-l: Why RDF increases as r increase instead of constant"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Tue, Nov 4, 2014 at 11:58 AM, Nifeng Guo hui <nifenggaohui_at_gmail.com> wrote:

*> Hey,
*

*> After I paly with RDF Plugin, I am still unsure about how properly use it.
*

*> First, "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. " Does this mean it is
*

*> not appropriate to treat all the 36 amino acids as one whole. Second, if my
*

*> conclusion that it is not appropriate to treat all the 36 amino acids an a
*

*> ball is validated, then does this explains why the RDF always increase from
*

*> starting until a suddenly dropped point as shown in my first plot. Third,
*

*> then what is the feature of "Use PBC" in the the Plugin?
*

please learn how a g(r) is computed and then we can discuss details.

your questions make little sense as they are.

*> Thanks.
*

*> Peng
*

*>
*

*> 2014-11-03 15:49 GMT-06:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
*

*>
*

*>> 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.
*

*>
*

*>
*

-- 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.

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