Hi priya , I am also have same problem...
>From my limited experience .. To solve these problem it is a good way to make index file of particular group (or molecule ) and then measure there g_mindist, g_gyrate and g_hbond You can get gyrate and hbond value for them... Have a nice Day ... With Best Wishes, Ram On Mon, Apr 9, 2012 at 6:02 PM, Justin A. Lemkul <[email protected]> wrote: > > > priya thiyagarajan wrote: > >> hello sir , >> >> i got few basic doubts in dynamics.. >> >> while performing analysis, we are calculating rmsd and gyrate for single >> molecule.. >> >> but in case of more molecules i.e by adding 20 molecules randomly using >> genbox , when we perform analysis, rmsd value we are obtaining is the >> average change in structure deviation from initial structure. >> >> what about gyrate?? >> >> i am getting one plot... how to interpret the result for 20 >> moecules..since 20 molecules arranged randomly, how it calculates the >> gyrate value.. >> >> please help me with your answer.. >> >> > I think g_polystat is more appropriate in this case. > > -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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