Hi Justin, Am using g_dist to find the distance between water and protein. for that i made a index file such as-
a CA(protein atoms) a OW(water atoms) i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35 instead of getting the result for protein-SOL distance . my output shows SOL-OW distance as seen below- t: 1 136 SOL 2336 OW 0.772373 (nm) even after specifying am getting an wrong output. Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > aiswarya pawar wrote: > >> Hi Users, >> >> Am using g_dist to find the distance between water and protein. but my >> output has the values of SOL-water distance. >> >> t: 1 136 SOL 2336 OW 0.772373 (nm) >> >> > This is not a water-water distance, it is the output of the -dist option > telling you that water molecule 136 has its OW atom at 0.7723273 nm from > whatever your reference group is. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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