So I used mindist for a certain group of molecules which is surrounded by water. I got plot number of contacts versuc sumulation time. According to what I see in a distance < 0.6nm at certain frame there are on average 150 contacts.
Actually how the programm calculates the number of contacts, if someone knows what is a creteria that a certain contact is formed? Is is a certain distance. best, Olga 2011/2/21 Olga Ivchenko <olga.ivche...@gmail.com> > Thank you very much. > best, > Olga > > 2011/2/21 Justin A. Lemkul <jalem...@vt.edu> > > >> g_mindist -on (with suitable index groups) should also do the trick. >> >> -Justin >> >> >> Erik Marklund wrote: >> >>> Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at >>> the moment. Version 4.0.x seem to work better. >>> >>> XAvier Periole skrev 2011-02-21 11.37: >>> >>>> g_dist >>>> On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: >>>> >>>> Dear Gromacs Users, >>>>> >>>>> I would like to know if there is in gromacs an option how to calculate >>>>> how many contacts has a certain atom i(n a molecules of interest) with >>>>> water >>>>> during the whole MD simulations (or at each step of MD). >>>>> Please could you advice me on this? >>>>> >>>>> best, >>>>> Olga >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>> >>> >> -- >> ======================================== >> >> 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 >> >> ======================================== >> >> -- >> 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 >> > >
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