Thank you!!
On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
