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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