[gmx-users] Bond distance and H bond

[Samith Rathnayake]

Dear sameer ,

1st you need to create a index file and group those specific atoms in this
file.

eg - make_ndx -f ../setup/b4em.pdb  -n index_Hdndx

then

a 1# (your specific atom, which u need to group)
a 2# (your specific atom, which u need to group)

( by the way you ought to know about the atom number which you desired  )


then you can use g_dist or gmx distance for evaluate the bond distance
between your specific atoms during the simulation.

eg-  g_dist -f .... -s ..... -n ..... -o .....

then it ask what are the groups (atoms)  u need to evaluate the distance



-cheers




On Sat, Oct 22, 2016 at 3:58 PM, Sameer Edirisinghe <nootsam at gmail.com>
wrote:

> Dear users,
>
> I need know how to find bond distance of H and O atoms of my polymer
> molecule system which contain 10 molecules in a box. I used to modify .top
> file .gro file to get 10 molecules in my system and i have successfully
> perform the production run.
>
> Then, I used following commands to find the bond distances to evaluate the
> H bond formation.
>
> 1) gmx make_ndx
>
> with above command, i need to know how to split 1 group into separate
> groups as all of molecules has packed in same .gro file.
>
>
> 2) gmx distance
>
> with above command im confusing how to select particular atom pair to find
> distance at the prompt after running command.
>
> Appreciate any guide here.
> --
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