[gmx-users] gmx hbond -tu error

[Justin Lemkul]

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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