Hi Daniel
Its solved :)
I should have used center2 also. Like this:
radial temp.dat 0.1 95 :K+ :1-389.O center2 volume intrdf temp_int.dat
Now I am getting almost same number of ions.
thanks
Jiomm
On Wed, Apr 9, 2014 at 6:17 PM, newamber list <newamberlist.gmail.com>wrote:
> Hi Daniel
>
>
> >> Bugfix 10 in particular fixed the normalization in the 'intrdf' plot
>
> I am using latest bug fix AMBER and AMBERTOOLS, so that must include
> bugfix 10.
>
> regards
> Jiomm
>
>
> On Wed, Apr 9, 2014 at 3:28 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi, what version of cpptraj are you using? Bugfix 10 in particular
>> fixed the normalization in the 'intrdf' plot.
>>
>> -Dan
>>
>>
>>
>> On Mon, Apr 7, 2014 at 8:33 PM, Jio M <jiomm.yahoo.com> wrote:
>> > Hi All
>> >
>> > I am using radial function to plot RDF of K ions around center of mass
>> of O atoms. I have around 2100 K+ ions and octahedron box (149.1524703
>> 149.1524703 149.1524703)
>> >
>> > radial temp.dat 0.1 95 :K+ :1-389.O volume intrdf temp_int.dat
>> >
>> >
>> > I should get almost exact number of K+ in my box after integrating. I
>> have following queries:
>> >
>> > 1) The integral values goes upto 1076448 which is too high. Also what
>> should be max bin size in this case to get expected number of ions? I have
>> chosen 95 because the RDF plot shows fall at 95 Angstroms (also it confuses
>> me as box size dimension goes upto 149 Angstroms and I should see a fall
>> around 140 or so)
>> >
>> > 2) Also I have one more query regarding 'volume' key word used here. In
>> manual it says
>> >
>> > ".. if the volume keyword is specified the density is determined from
>> the average volume of the system over all Frames."
>> >
>> > So in this case does this mean density is a 'number density' which is =
>> (total number of K+ ions in a box / avg. volume of box)
>> >
>> > thanks
>> > JIom
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Apr 09 2014 - 11:00:06 PDT
