[gmx-users] Reducing Standard Error output

[Tsjerk Wassenaar]

Hi Jack,

The option -v is for verbose output.
The LINCS warnings may indicate an issue regarding the stability of
your system. They usually precede crashes. Maybe you need to
equilibrate a bit further.

Hope it helps,

Tsjerk

On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz <js at drugdiscoveryathome.com> wrote:
> Our first run typically produces this output
>
> Getting Loaded...
> Reading file md.tpr, VERSION 4.0.5 (single precision)
> Loaded with Money
>
> starting mdrun 'Protein in water'
> 500 steps,      1.0 ps.
>
> step 0
> step 100, remaining runtime:    95 s          Fraction complete: 0.2
>
> step 200, remaining runtime:    70 s          Fraction complete: 0.4
>
> step 300, remaining runtime:    46 s          Fraction complete: 0.6
>
> step 400, remaining runtime:    23 s          Fraction complete: 0.8
>
> Writing final coordinates.
>
> step 500, remaining runtime:     0 s          Fraction complete: 1
>
>        Parallel run - timing based on wallclock.
>
>               NODE (s)   Real (s)      (%)
>       Time:    119.000    119.000    100.0
>                       1:59
>               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:     55.372      3.138      0.728     32.990
>
> gcq#0: Thanx for Using GROMACS - Have a Nice Day
>
>
> For our project's workflow we are extending the simulations using
> these arguments,
> -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md
>
> but I notice there is much more standard error output than I was
> expecting, in addition to a LINCS WARNING. Should I be worried about
> that warning?
> Is there a way we can turn off these error reports for each timestep?
>
> Step 785, time 1.57 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.051275, max 3.234419 (between atoms 2396 and 2397)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   2396   2397  103.7    0.0973   0.4065      0.0960
>
> Step 786, time 1.572 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000031, max 0.001926 (between atoms 2396 and 2397)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   2396   2397   69.5    0.4065   0.0962      0.0960
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist