[gmx-users] error message in mdrun: Check for bad contacts and/or reduce the timestep if appropriate.
nizar.fkub08 at gmail.com
Sun May 4 17:44:51 CEST 2014
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
More information about the gromacs.org_gmx-users