[gmx-users] Occupancy for a distance cut off

[ram bio]

Thank you!!

On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/11/13 9:16 PM, ram bio wrote:
>>
>> Hi Justin,
>>
>> Thanks for the suggestion.
>>
>> I executed the following command:
>>
>> g_dist -f n101c2naclprod2-12nsvrpr.trr -s
>> n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35  -o
>> N101Cbest2NACL606S336HG1.xvg
>>
>> and the output was distance calculated for every 10 frames in nm as under:
>>
>> t: 11870  336 SER 4166 HG1  0.239086 (nm)
>> t: 11880  336 SER 4166 HG1  0.248868 (nm)
>> t: 11890  336 SER 4166 HG1  0.231819 (nm)
>> t: 11900  336 SER 4166 HG1  0.218495 (nm)
>> t: 11910  336 SER 4166 HG1  0.233166 (nm)
>> t: 11920  336 SER 4166 HG1  0.283512 (nm)
>> t: 11930  336 SER 4166 HG1  0.239512 (nm)
>> t: 11940  336 SER 4166 HG1  0.216938 (nm)
>> t: 11950  336 SER 4166 HG1  0.220066 (nm)
>> t: 11960  336 SER 4166 HG1  0.227595 (nm)
>> t: 11970  336 SER 4166 HG1  0.247895 (nm)
>> t: 11980  336 SER 4166 HG1  0.259074 (nm)
>> t: 11990  336 SER 4166 HG1  0.228319 (nm)
>> t: 12000  336 SER 4166 HG1  0.264722 (nm)
>>
>> So, my question is that now  do maths and find percent frames that
>> were above the 3.5 Å and expresses it relation to unity for occupancy.
>> That is if i have 30 frames above 3.5Å out of 100, then the occupancy
>> would be 0.7.
>>
>> Please advice if there is any other ways to do it..
>>
>
> Redirect the output into a file, count the number of lines in the file with
> wc -l and you have the answer.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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