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 <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
