[gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Wait, now I remember, you even approached me in a private message and we
exchanged quite a few emails. Did you try any of my suggestions? No success?

J

On Thu, Nov 23, 2017 at 7:36 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> Hi,
>
> I clearly remember replying to something similar sometime ago, and I'm
> almost sure the post was yours. It may be a good idea to rummage through
> the mailing list, because I'm pretty sure this type of analysis has been
> discussed here more than once.
>
> Cheers,
> J
>
> On Thu, Nov 23, 2017 at 4:41 PM, 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-gma
>> il-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.
>>
>
>