On Sun, Sep 18, 2011 at 7:25 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > > >> >> On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Steven Neumann wrote: >> >> >> >> On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham >> <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.**au<mark.abra...@anu.edu.au> >> > >> <mailto:mark.abra...@anu.edu._**_au >> <mailto:mark.abra...@anu.edu.**au <mark.abra...@anu.edu.au>>>> >> wrote: >> >> On 19/09/2011 2:02 AM, Steven Neumann wrote: >> >> Hi Gromacs Users, >> Can anyone explain me why in g_bond the distance is takes >> <= 3.5nm. >> >> >> If you mean g_hbond, and are using units incorrectly, 0.35nm >> would >> be a characteristic distance cut-off for deciding whether a >> hydrogen >> bond might exist.... >> >> That is what I already know... >> >> >> It is said that it comes from the first minimum o RDF of >> Oxygen >> atoms in SPC water model. I am sorry, but I just do not >> catch >> this. Thank you in advance. >> >> >> Said where? About what? :) >> >> Mark >> >> About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure >> 8.3 - RDF of O-O atoms in SPC water model. Can you explain this >> 0.35 nm value as a first minima? >> >> >> It's there in Figure 8.3, a shallow minimum at 0.35 nm. For this to >> occur, then ideally the water molecules are forming H-bonds >> (O-H...O) with an O-O distance of 0.35 nm. Moreover (and I know I >> posted this to the list before, so it's in the archive in greater >> detail somewhere), the geometric criteria used by g_hbond are >> generally accepted as indicative of hydrogen bonding from >> crystallographic studies. >> >> -Justin >> >> Thank you Justin. But I do not get why it is first minimum of RDF? I >> thought it has to be first maximum of this function - the highest particle >> density? >> >> > Right, the minimum defines the cutoff at which hydrogen bonding is less > likely. So the hydrogen bonds should all be within 0.35 nm, not occurring > at 0.35 nm. Apologies for my somewhat confusing reply earlier, my mind was > going faster than my typing :) The O-O distance of 0.35 nm represents an > upper bound for a hydrogen bond to occur, not that this is the most > populated distance for hydrogen bonding. > > -Justin > Thank you Justin, that helped a lot! Easy explanations makes life very simple! :) > > >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>**> >> >> >> >> >> http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> > >> >> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> > >> >> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> > >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org/> >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >>. >> >> Can't post? Read >> >> http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists> >> >> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> > >> >> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> >> -- ==============================**__========== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <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 >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > 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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