Hi friends, I am calculating free energy of a protein. I got this message when i run mdrun. My command was mdrun -deffnm npt -nt 1
Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000022, max 0.000500 (between atoms 2240 and 2243) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2844 2845 39.8 0.1105 0.1090 0.1090 step 2: Water molecule starting at atom 41058 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have reduced nsteps from 5000 to 10000, but the same error message appeared ================================================= My Best Regards, Nizar Medical Faculty of Brawijaya University, Malang, Indonesia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
