[gmx-users] g_hbond

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 17 17:37:27 CEST 2010

Fahimeh Baftizadeh Baghal wrote:
> hello,
> I have a trajectory generated by gromacs in which I excluded water and 
> there is only protein, now I like to see how does the number of h_bond 
> between water and protein change during the trajectory. In fact when I 
> use g_hbond I can choose the water and protein but I was wondering where 
> does the information about water come from??

Certainly you can choose whatever groups are present (either from default groups 
or from those in an index file), but I would imagine the command will either 
fail or simply identify that there are no hydrogen bond donors or acceptors 
within what would otherwise be water.

If you have not saved the coordinates for water, you cannot run any command to 
analyze properties related to or involving water.


> thank you in advance for your time
> Fahimeh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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