Hi,
If you use the 'normdensity' keyword and specify bulk density (with
'density <#>' with units of molecules/Ang^3) the isovalue of 1 will be
bulk.
Hope this helps,
-Dan
On Wed, Jul 26, 2017 at 10:55 AM, maryvj1985 <maryvj1985.gmail.com> wrote:
>
> Thank you very much for the reply.
>
> I will try this option.
>
> Are you familiar with grid analysis of Na+ ions in a simulation.
> I have done a grid analysis. But I don't understand what range if isovalue should I specify. Like in the case of water analysis you say 2 times bulk water density.
> My system has 0.3 M NaCl added.
>
> Mary
>
>
> Sent from: Lenovo S90-A
>
> On Jul 26, 2017 7:16 PM, George Giambasu <giambasu.gmail.com> wrote:
>>
>> Sure - you can ask cpptraj to compute an RDF (radial distribution
>> function) between (i) mask and (ii) Na+. Next, integrate that RDF up to
>> the specified distance ((using xmgrace for example)) to get the desired
>> ion count.
>>
>>
>> As for the second question, ions should be imaged too. If you have
>> doubts output the imaged trajectory and visualize it in vmd.
>>
>> George
>>
>>
>> Mary Varughese wrote:
>> > Hi
>> >
>> > I have some ions related doubts
>> >
>> > *Is it possible to count Na+ ions with in the 3.6 A distance of atoms
>> > specified with in a mask?
>> >
>> > *In the below command does ions also get imaged along with water (I want to
>> > do grid analysis of Na+ ions)
>> >
>> > center :1-12 mass origin
>> > image origin center familiar
>> > center :1-24 mass origin
>> > image origin center familiar
>> >
>> >
>> > Thanking you
>> >
>> >
>> > mary
>> > _______________________________________________
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>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Dr. George M. Giambasu
>> Rutgers, The State University of New Jersey
>> 174 Frelinghuysen Road, Room 308E Piscataway,
>> NJ 08854, USA giambasu.rutgers.edu
>> www.rci.rutgers.edu/~giambasu
>> Office: 1-848-445-5223 Cell: 1-612-644-8285
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jul 26 2017 - 09:00:03 PDT
