[gmx-users] Regarding calculating the water orientation profile

[Mark Abraham]

Hi,

Why do you want to do something when you don't understand what it is or
whether it will be useful?

Mark

On Fri, Nov 24, 2017 at 9:08 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> So what exactly does this Orientation Profile means.??
> I am really confused with the exact approach towards it...
>
>
> <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 Fri, Nov 24, 2017 at 12:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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.dilip at 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.abraham at 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.dilip at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.