GROMACS version:2018
GROMACS modification: Yes/No
Here post your question : I am trying to do adsorption of cysteine and au atoms on the Au (111) surface in the prescence of water but when i tired to run nvt,lincs warning is coming, i have also done minimization again for a longer time step but this is occuring again.
gmx mdrun -v -deffnm nvt
Using 1 MPI thread
Using 8 OpenMP threads
WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.
starting mdrun ‘Cysteine adsorbed on gold surface in water’
5000000 steps, 10000.0 ps.
step 0
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.177076, max 2.771672 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.0983 0.3708 0.0983
Wrote pdb files with previous and current coordinates
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016433, max 0.257216 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.3708 0.1236 0.0983
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.185686, max 2.906452 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.1236 0.3840 0.0983
Wrote pdb files with previous and current coordinates
Step 4, time 0.008 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016691, max 0.261248 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.3840 0.1240 0.0983
Step 5, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.182154, max 2.851163 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.1240 0.3786 0.0983
Wrote pdb files with previous and current coordinates
Step 6, time 0.012 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018188, max 0.284685 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.3786 0.1263 0.0983
Step 7, time 0.014 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.175252, max 2.743125 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.1263 0.3679 0.0983
Wrote pdb files with previous and current coordinates
Step 8, time 0.016 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.032851, max 0.514203 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.3679 0.1488 0.0983
Wrote pdb files with previous and current coordinates
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.178510, max 2.794117 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1639 1640 90.0 0.1488 0.3730 0.0983
Wrote pdb files with previous and current coordinates
Step 10, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034749, max 0.534709 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 90.0 0.0983 0.1081 0.0983
1639 1640 90.0 0.3730 0.1509 0.0983
Wrote pdb files with previous and current coordinates
Step 11, time 0.022 (ps) LINCS WARNING
relative constraint deviation after LINCS:pls
rms 0.157708, max 2.468521 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 51.2 0.1081 0.0983 0.0983
1639 1640 90.0 0.1509 0.3410 0.0983
Wrote pdb files with previous and current coordinates
Step 12, time 0.024 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034603, max 0.541625 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 66.2 0.0983 0.0983 0.0983
1639 1640 90.0 0.3410 0.1515 0.0983
Wrote pdb files with previous and current coordinates
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.155060, max 2.426614 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 90.0 0.0983 0.1029 0.0983
1639 1640 90.0 0.1515 0.3368 0.0983
Wrote pdb files with previous and current coordinates
Step 14, time 0.028 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033753, max 0.524486 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 90.0 0.1029 0.1045 0.0983
1639 1640 90.0 0.3368 0.1499 0.0983
Wrote pdb files with previous and current coordinates
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.154221, max 2.413945 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 72.5 0.1045 0.0983 0.0983
1639 1640 90.0 0.1499 0.3356 0.0983
Wrote pdb files with previous and current coordinates
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034276, max 0.536503 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 75.0 0.0983 0.0983 0.0983
1639 1640 90.0 0.3356 0.1510 0.0983
Wrote pdb files with previous and current coordinates
Step 17, time 0.034 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.156050, max 2.442397 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 90.0 0.0983 0.1011 0.0983
1639 1640 90.0 0.1510 0.3384 0.0983
Wrote pdb files with previous and current coordinates
Step 18, time 0.036 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034630, max 0.539574 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 90.0 0.1011 0.1034 0.0983
1639 1640 90.0 0.3384 0.1513 0.0983
1643 1644 52.6 0.1090 0.1090 0.1090
1648 1649 50.8 0.1090 0.1090 0.1090
Wrote pdb files with previous and current coordinates
Step 19, time 0.038 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.162397, max 2.541919 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 80.6 0.1034 0.0983 0.0983
1639 1640 90.0 0.1513 0.3482 0.0983
1643 1644 38.6 0.1090 0.1090 0.1090
1648 1649 37.9 0.1090 0.1090 0.1090
Wrote pdb files with previous and current coordinates
Step 20, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033840, max 0.525755 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 90.0 0.0983 0.1046 0.0983
1639 1640 90.0 0.3482 0.1500 0.0983
1643 1644 32.2 0.1090 0.1090 0.1090
1648 1649 32.3 0.1090 0.1091 0.1090
Wrote pdb files with previous and current coordinates
Step 21, time 0.042 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.149554, max 2.340898 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 63.8 0.1046 0.0983 0.0983
1639 1640 90.0 0.1500 0.3284 0.0983
Wrote pdb files with previous and current coordinates
Step 22, time 0.044 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.031706, max 0.496276 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 72.4 0.0983 0.0983 0.0983
1639 1640 90.0 0.3284 0.1471 0.0983
Step 23, time 0.046 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.154518, max 2.418583 (between atoms 1639 and 1640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 73.4 0.0983 0.0983 0.0983
1639 1640 90.0 0.1471 0.3360 0.0983
Wrote pdb files with previous and current coordinates
Step 24, time 0.048 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.311879, max 14.591803 (between atoms 1643 and 1644)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 73.1 0.0983 0.0983 0.0983
1639 1640 90.0 0.3360 0.1269 0.0983
1643 1644 90.0 0.1090 1.6995 0.1090
1648 1649 90.0 0.1089 1.6835 0.1090
1648 1650 47.1 0.1090 0.1138 0.1090
Wrote pdb files with previous and current coordinates
Step 25, time 0.05 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 2.205048, max 30.697865 (between atoms 1648 and 1649)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 77.0 0.0983 0.0983 0.0983
1639 1640 90.0 0.1269 0.3415 0.0983
1643 1644 90.0 1.6995 1.8073 0.1090
1648 1649 90.0 1.6835 3.4551 0.1090
1648 1650 90.0 0.1138 0.1232 0.1090
Wrote pdb files with previous and current coordinates
Step 26, time 0.052 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.999236, max 27.372278 (between atoms 1643 and 1644)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 74.9 0.0983 0.0983 0.0983
1639 1640 90.0 0.3415 0.1150 0.0983
1643 1644 90.0 1.8073 3.0926 0.1090
1648 1649 90.0 3.4551 1.7060 0.1090
1648 1650 90.0 0.1232 0.5357 0.1090
Wrote pdb files with previous and current coordinates
Step 27, time 0.054 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 253.982407, max 3973.138184 (between atoms 1648 and 1650)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1429 1430 84.0 0.0983 0.0983 0.0983
1639 1640 90.0 0.1150 0.3506 0.0983
1643 1644 90.0 3.0926 2.1388 0.1090
1645 1646 34.5 0.1020 0.1022 0.1020
1648 1649 84.3 1.7060 14.7535 0.1090
1648 1650 90.0 0.5357 433.1810 0.1090
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
pls tell me why it is happening, i have upload nvt.mdp file here also for your convenience:
npt.mdp (2.5 KB)