Hello Jonathan, Suppose i want to calculate the cos theta distribution of hydrogen's of water in 1st hydration shell of amino acid (glycine) ie., orientation of alpha carbon of glycine with oxygen of water molecules... how can i calculate it..??
And in what groups/atoms should i make the indexes..?? (like it says the index file must contain atom triplets for angles)... How to make the atom triplets.. which atom the cos theta is to be found out should be placed in the indexing order.. so to find the angle between alpha carbon of glycine with oxygen of water molecules.... <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Wed, Apr 12, 2017 at 11:12 AM, Jonathan Saboury <jsab...@gmail.com> wrote: > For making .ndx files look at the following: > http://manual.gromacs.org/programs/gmx-make_ndx.html > > Best of luck, > Jonathan > > On Tue, Apr 11, 2017 at 10:26 PM, Dilip H N <cy16f01.di...@nitk.edu.in> > wrote: > > > gmx sorient -f .xtc/trr -s .tpr -n .ndx... > > > > How to make these indexes for this case..?? what are the atoms/groups > > that i need to consider for > > > > indexing in this case.. > > > > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > <https://mailtrack.io/install?source=signature&lang=en&; > > referral=cy16f01.di...@nitk.edu.in&idSignature=22> > > > > On Wed, Apr 12, 2017 at 9:57 AM, Dilip H N <cy16f01.di...@nitk.edu.in> > > wrote: > > > > > Hello, > > > 1] I want to calculate cos theta distributions (eg.,cos theta > > > distributions of hydrogen's of water in first hydration shell layer of > > > amino acid)..?? > > > 2] and how can i analyze the graph ..?? > > > -- > > > With Best Regards, > > > > > > DILIP.H.N > > > Ph.D Student > > > > > > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > > <https://mailtrack.io/install?source=signature&lang=en&; > > referral=cy16f01.di...@nitk.edu.in&idSignature=22> > > > > > > > > > > > -- > > With Best Regards, > > > > DILIP.H.N > > Ph.D Student > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
