[gmx-users] How to solve the "LINCS WARNING" problem
변진영
byunjy0614 at gmail.com
Tue Apr 14 08:31:05 CEST 2020
Dear GROMACS users,
Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below
Step 231785, time 463.57 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3035 3036 34.0 0.1090 0.1087 0.1090
….
Step 231825, time 463.65 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3024 3025 90.0 0.1090 0.1236 0.1090
3026 3027 100.8 0.1090 6.6242 0.1090
3028 3029 162.5 1.7683 5245.4102 0.1090
3033 3034 106.7 0.1090 426.5654 0.1090
3035 3037 90.0 0.3851 0.7991 0.1090
3038 3039 90.0 0.6045 0.4497 0.1090
3038 3040 90.0 0.1123 0.2833 0.1090
3041 3042 59.0 0.1020 0.1020 0.1020
Wrote pdb files with previous and current coordinates
Step 231826, time 463.652 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1423 1424 140.4 0.1000 503.9983 0.1000
3024 3025 61.1 0.1236 223337872.0000 0.1090
3026 3027 168.8 6.6242 149263.5000 0.1090
3028 3029 165.8 5245.4102 263929.4375 0.1090
3031 3032 116.2 0.1090 223428336.0000 0.1090
3033 3034 179.9 426.5654 446766720.0000 0.1090
3035 3036 35.3 29.6105 831.0708 0.1090
3035 3037 102.9 0.7991 775.3371 0.1090
3038 3039 90.0 0.4497 0.6355 0.1090
3038 3040 47.7 0.2833 0.1111 0.1090
step 231826: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms.
Why does the LINCS warning occurs? and How I solve this problem?
Many Thanks
Jinyoung
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