Hi, I have no idea what a cos theta distribution is, nor the objective of your study, so it's hard to help. But gmx mk_angndx is intended to help with such cases.
Mark On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > 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. > -- 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.