[gmx-users] Reducing Standard Error output

[Jack Shultz]

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