[gmx-users] gmx hbond -tu error

[Mark Abraham]

Hi,

A quick glance at the code suggests Justin is right. You should be able to
inspect the output of gmx hbond and see that in fact -e means that many
fewer trajectory frames are being read.

Mark

On Tue, May 2, 2017 at 2:56 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/1/17 10:15 AM, Marcelo Depólo wrote:
> > Hi!
> >
> >
> > I am running ACF calculations in gmx hbond tool in 5.0.7 version.
> >
> > When running:
> >
> > gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg
> >
> > and
> >
> > gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 10000 -ac acf_0-10ns.xvg
> >
> >
> > The results given for the ACF are completely different (example: CHI^2 =
> > 0.000347 and CHI^2 = 22.9131, respectively). It seems -tu flag is not
> > working properly here.
> >
> > Still, all graphs generated make sense (going until 5ns, the half of
> > trajectory time analyzed).
> >
> > Does anyone already encountered this error?
> >
>
> The -tu option only alters output time values, not the arguments on the
> command
> line, IIRC.  The help info does specify that -b and -e take time in ps.
> This is
> somewhat non-intuitive, but the behavior is consistent with the
> documentation.
>
> -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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