[gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

Hi,

Yes,
http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
is
the fix for another bug that could in principle produce this behaviour, but
semiisotropic is supposed to take two real values, so something may be
amiss here.

Mark

On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
> > Dear All,
> >
> > when using gmx-5.1.2 with a mdp file with the following pressure
> coupling parameters:
> >
> > ; pressure coupling
> > Pcoupl                   = berendsen
> > Pcoupltype               = semiisotropic
> > nstpcouple               = -1
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau_p                    = 5 5
> > compressibility          = 4.5e-5 4.5e-5
> > ref_p                    = 1.0 1.0
> > ; Scaling of reference coordinates, No, All or COM
> > refcoord_scaling         = all
> >
> >
> > grompp gives the error message:
> >
> >
> > ERROR 1 [file parameter.mdp, line 387]:
> >    Right hand side '5 5' for parameter 'tau_p' in parameter file is not a
> >    real value
> >
> >
> > With versions below 5.1.2 everything seems to be fine. Are there
> additional changes beyond what is mentioned in the release notes or am I to
> blind to find the right section?
> >
>
> tau_p only takes one value (unlike tau_t, which needs one per thermostat
> group).
>   The issue that was fixed was grompp silently ignoring extraneous input
> values,
> so previous versions carry on happily ignoring the stuff it doesn't need.
>
>
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
>
> -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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