[gmx-users] Occupancy for a distance cut off

[ram bio]

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..

Thanks,
Pramod

On Mon, Feb 11, 2013 at 7:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/11/13 6:15 PM, ram bio wrote:
>>
>> Dear Gromacs Users,
>>
>> I have a run a MD simulation on protein bound with ligand and ions
>> using Gromacs 4.5.4. I am able to calculate the distances between ions
>> and coordinating residues using g_dist. The output is in the form of
>> xvg file, but I am looking for the occupancy for a cut off distance
>> (3.5 Å) between ion and a particular residue atom during simulation.
>> Please suggest.
>>
>
> g_dist -dist 0.35
>
> -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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists