[gmx-users] Hydrogen bond calculation

[Dallas Warren]

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html
http://manual.gromacs.org/documentation/2019.1/onlinehelp/selections.html
http://manual.gromacs.org/documentation/2019.1/onlinehelp/selections.html#selection-examples

Select water and osmolyte within the specified distance from the protein,
that equates to the first hydration shell distance, make the index of that,
the run hydrogen bond analysis using those.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 27 Feb 2019 at 03:37, ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> Dear all,
> I have done the MD simulation of protein-water-osmolyte. Now I want to
> calculate the number of hydrogen bond formed between water and osmolyte in
> the first hydration shell of the protein. Can anyone tell me how to
> calculate this?
> Do I have to make the index of water and osmolytes molecule in the first
> hydration shell? How do I make the index? kindly advise the proper steps.
> Thank you
> --
> Ishrat Jahan
> Research Scholar
> Department Of Chemistry
> A.M.U Aligarh
> --
> 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.
>