Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run.
Jack On Thu, Dec 3, 2009 at 10:36 AM, Tsjerk Wassenaar <[email protected]> wrote: > 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 > -- 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
