[gmx-users] LINCS error in MD simulation

f vazifeshenas fahim.vazifeshenas at gmail.com
Sun Apr 10 08:48:04 CEST 2016

Dear all
I am trying to Run one protein with ligand and i am getting a note and an
error as fallows:

Step 5009957, time 10019.9 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000219, max 0.005436 (between atoms 2836 and 2835)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2836   2835   90.0    0.1236   0.1005      0.1000

Program gmx, VERSION 5.0.5
Source code file: /home/soft/gromacs-5.0.5/src/gromacs/mdlib/constr.c,
line: 224

Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Does anybody know to deal with this LINCS error?

Best regard

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