hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms.
Thanks On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul <[email protected]> wrote: > > > aiswarya pawar wrote: > >> Hi gromacs Users, >> >> 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) >> can anyone tell me whats wrong with this. >> > > Please see my previous message. This is not a "SOL-water" distance. > > -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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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