VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 04 2013 - 08:51:50 CST

On Mon, Nov 4, 2013 at 2:47 PM, bharat gupta <bharat.85.monu_at_gmail.com> wrote:
>
> Sir,
>
> Sorry for not framing my question properly. What I want is a final number
> for density around those residues. For eg, in this thread some one has

no. you are not paying attention. there *is* no such single number. it
cannot be. full stop. all there is are the various density values
through space as recorded at the various grid points. that is not the
same.

> pointed out the values that were obtained after doing volmap calculations :
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14404.html

but that person is very clearly referring to individual grid points
and not a single number. so that is *not* what you are asking for. as
i explained now twice, the property you ask for is ill defined. you
*do* have all the density values averaged over all the grid points in
the dx file. that is it. if you want to extract a single number out of
that, you first have to explain how this could be done in a consistent
and reproducible fashion without depending significantly on the grid
spacing and enclosing volume.

you have - so far - failed to explain this, so you cannot expect to
get any better answer than those that you already got. before you keep
asking the same thing all over again, please first prove how the
number you are looking for *can* be computed.

axel.

>
>
>
> On Mon, Nov 4, 2013 at 10:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Nov 4, 2013 at 1:41 PM, bharat gupta <bharat.85.monu_at_gmail.com>
>> wrote:
>> >
>> >
>> >
>> > Thanks for the reply Sir,
>> >
>> > I got the volmap.dx file and I visualized it also, using Isosurface
>> > representation. But I want to know that final average value . I checked
>> > the
>> > volmap.dx file there are three columns with lots of zeros and sometimes
>> > some
>> > values ... But still I didn't find the way to get the averaged value ??
>>
>> i don't understand the question. these numbers *are* the averaged
>> values. one for every grid point.
>>
>> axel.
>>
>>
>> >
>> >
>> > On Mon, Nov 4, 2013 at 9:24 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> > wrote:
>> >>
>> >> On Mon, Nov 4, 2013 at 11:49 AM, bharat gupta
>> >> <bharat.85.monu_at_gmail.com>
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > I have used the volmap plugin to calculate the water density around
>> >> > residues
>> >> > 115-118 of my protein. I checked it by displaying it as an
>> >> > isosurface. I
>> >> > want to know whether is it possible to get the final average value
>> >> > (i.e.
>> >> > water density averaged over all time steps) used to depict the plot??
>> >>
>> >> yes, if you check the "compute for all frames" button.
>> >>
>> >> http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/
>> >>
>> >> you can have the final data either added to your molecule or saved as
>> >> a .dx file.
>> >>
>> >> axel.
>> >>
>> >> >
>> >> >
>> >> > Thanks in advance for help..
>> >> >
>> >> > Regards
>> >> > -----
>> >> > Bharat
>> >>
>> >>
>> >>
>> >> --
>> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> >> International Centre for Theoretical Physics, Trieste. Italy.
>> >
>> >
>> >
>> >
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
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> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.