# Lincs warning in nvt **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, mdrun\ **Created:** [February 24, 2023, 11:06am UTC](https://gromacs.bioexcel.eu/t/lincs-warning-in-nvt/5864 "2023-02-24T11:06:49Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![parul](https://avatars.discourse-cdn.com/v4/letter/p/5fc32e/32.png) [@parul](https://gromacs.bioexcel.eu/u/parul)\ **Post date:** [February 24, 2023, 11:06am UTC](https://gromacs.bioexcel.eu/t/lincs-warning-in-nvt/5864/1 "2023-02-24T11:06:49Z")
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](https://gromacs.bioexcel.eu/uploads/short-url/Agzrp1R0hhSxBdyHIHBkx6J4aFU.mdp) (2.5 KB)