Hi, "Coming closer" implies you care about distance, but your original question was about orientation. So it's unclear what you want.
Mark On Thu, 23 Nov 2017 16:50 Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > I want to calculate whether the water molecules are coming closer towards > the N-terminal or towards the C-terminal of the amino-acid throughout the > simualtion. > And hence it can shed some light on the Hydrogen bond > dynamics....hopefully... > > Thank you > > > > <https://mailtrack.io/> Sent with Mailtrack > < > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality > > > > On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > It sounds like to need to be more clear about what you want to calculate > > before you can sensibly find a tool to do it. You should be able to write > > down the equation for what you want to compute as your observation long > > before you run a simulation, or how will you know what data to collect? > > > > Mark > > > > On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > > > > > Hello Sir, > > > I have run a simulation of amino-acid (glycine) with water molecules > for > > 10 > > > ns. Now i need to find out/analyze that whether the water molecules are > > > getting/more oriented towards N-terminal of glycine or towards the > > > C-terminal of glycine. (i hope this is what water orientation profile > > means > > > ie., the preferential orientation of water towards particular > > > moeity/group...). > > > So, which is the exact module/command to find this..?? wether gmx > sorient > > > or gmx gangle or gmx angle ..?? > > > > > > How to resolve this issue... > > > > > > Thank you > > > > > > > > > -- > > > With Best Regards, > > > > > > DILIP.H.N > > > Ph.D Student > > > > > > > > > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > > < > > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ > > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_ > > medium=signature&utm_campaign=signaturevirality > > > > > > > -- > > > 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.