[gmx-users] find hbond between different groups during simulation

[Mark Abraham]

Hi,

Yes that's life. It's nearly impossible to do research and never have to
build your own tools from parts!

Mark

On Thu, 21 Jan 2016 07:12 Mahboobe Sadr <sadr.mahboobe1989 at gmail.com> wrote:

>   Does it mean,  i can't do that automatically??
>
>
>
> On Thursday, January 21, 2016, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > On 1/20/16 4:08 AM, Mahboobe Sadr wrote:
> >>
> >> Dear all,
> >>
> >> I want to find hydrogen bonds between waters and The protein. since in
> each
> >> frame I selected some specifc waters, I want to find hydrogen bonds
> during
> >> simulation for different waters(which are in the pore of the protein)
> and
> >> the protein.
> >>   as  "g_hbond" doesn't any option like "-select" in "gmx distance", I
> >> couldn't find the hbond i want.
> >>
> >
> > Use gmx select to get per-frame index groups that satisfy the selection
> criteria, then run the analysis frame by frame.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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