[gmx-users] h_bonds

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 14 07:46:34 CET 2014

On Mar 14, 2014 4:27 AM, "virk" <virkblitz at yahoo.com> wrote:
> Dear Justin,
> Thanks for feedback...The percentage of glycine molecules that
> exist as monomers (i.e., with no hydrogen bonding to any
> other glycine molecule), dimers (i.e., pairs of glycine
> molecules hydrogen bonded to each other but not to any other
> glycine molecule), and trimers (i.e., groups of three glycine
> molecules hydrogen bonded to each other but not to any other
> glycine molecule).

Now you have definitions that can be implemented (whether they are the
right definitions is your call). Unfortunately, they are complex.
Identifying putative dimers is straightforward, but pruning the list of
higher-order associations requires identifying that each member of a
putative dimer is a member of no other dimer. g_select is good for the
former (but you probably have to define a hydrogen bond criterion
yourself), but I don't know if it can do the next stage, even in a second
call. If not, then you will need to write a script - which you would need
anyway if you were to try to use g_hbond.


> I am using default h-bond criteria 0.35 nm but that can
> be changed accordingly.
> Amninder virk
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