Simulation pause at about 80-100 step for chignolin

[Frank-LIU-520]

I followed the 'Get Start' instruction to run a MD for chignolin. However it can not proceed after about 80 steps with the warning Solvent dynamic component Tinker terminated abnormally, cannot proceed.. What should I do?

Details: Command line: "./ai2bmd --prot-file chig.pdb --preprocess-dir chig_preprocessed --preeq-steps 0 --sim-steps 1000 --record-per-steps 1" GPU: NVIDIA GeForce RTX 3090 OS: Ubuntu 20.04.6 LTS Docker: Docker version 27.1.2

OUTPUT DeviceStrategy: setting strategy to [small-molecule / combined] ERROR:root:tinker-GPU is specified, but there's no GPU. Reverting back to CPU. Preprocessing step already done, skip... run_preprocess takes 0.2249157428741455 seconds Loading models... Start simulation for 1000 steps Step 0: Epot = -129456.773eV Ekin = 688.941eV Etot = -128767.832eV Step 1: Epot = -129495.345eV Ekin = 724.111eV Etot = -128771.234eV Step 2: Epot = -129566.198eV Ekin = 789.967eV Etot = -128776.231eV Step 3: Epot = -129598.216eV Ekin = 822.229eV Etot = -128775.987eV Step 4: Epot = -129598.440eV Ekin = 825.653eV Etot = -128772.787eV Step 5: Epot = -129612.714eV Ekin = 837.533eV Etot = -128775.182eV Step 6: Epot = -129625.972eV Ekin = 847.866eV Etot = -128778.107eV Step 7: Epot = -129596.541eV Ekin = 819.423eV Etot = -128777.118eV Step 8: Epot = -129534.537eV Ekin = 761.545eV Etot = -128772.992eV Step 9: Epot = -129501.501eV Ekin = 731.050eV Etot = -128770.452eV Step 10: Epot = -129534.765eV Ekin = 761.559eV Etot = -128773.206eV Step 11: Epot = -129599.201eV Ekin = 820.766eV Etot = -128778.434eV Step 12: Epot = -129634.611eV Ekin = 855.326eV Etot = -128779.286eV Step 13: Epot = -129640.745eV Ekin = 863.866eV Etot = -128776.878eV Step 14: Epot = -129655.990eV Ekin = 877.433eV Etot = -128778.557eV Step 15: Epot = -129672.862eV Ekin = 891.577eV Etot = -128781.285eV Step 16: Epot = -129653.018eV Ekin = 871.709eV Etot = -128781.309eV Step 17: Epot = -129594.452eV Ekin = 816.439eV Etot = -128778.013eV Step 18: Epot = -129550.091eV Ekin = 775.125eV Etot = -128774.966eV Step 19: Epot = -129566.279eV Ekin = 789.375eV Etot = -128776.904eV Step 20: Epot = -129622.065eV Ekin = 840.169eV Etot = -128781.896eV Step 21: Epot = -129655.988eV Ekin = 871.981eV Etot = -128784.006eV Step 22: Epot = -129653.208eV Ekin = 871.409eV Etot = -128781.798eV Step 23: Epot = -129654.457eV Ekin = 872.827eV Etot = -128781.631eV Step 24: Epot = -129667.680eV Ekin = 883.595eV Etot = -128784.085eV Step 25: Epot = -129657.169eV Ekin = 871.864eV Etot = -128785.305eV Step 26: Epot = -129607.404eV Ekin = 824.785eV Etot = -128782.618eV Step 27: Epot = -129555.005eV Ekin = 775.848eV Etot = -128779.156eV Step 28: Epot = -129549.702eV Ekin = 770.331eV Etot = -128779.371eV Step 29: Epot = -129592.846eV Ekin = 809.599eV Etot = -128783.247eV Step 30: Epot = -129636.278eV Ekin = 849.728eV Etot = -128786.550eV Step 31: Epot = -129646.069eV Ekin = 860.401eV Etot = -128785.669eV Step 32: Epot = -129644.614eV Ekin = 859.336eV Etot = -128785.278eV Step 33: Epot = -129655.668eV Ekin = 868.655eV Etot = -128787.013eV Step 34: Epot = -129659.041eV Ekin = 870.171eV Etot = -128788.870eV Step 35: Epot = -129626.131eV Ekin = 838.435eV Etot = -128787.697eV Step 36: Epot = -129572.651eV Ekin = 788.652eV Etot = -128784.000eV Step 37: Epot = -129553.920eV Ekin = 770.873eV Etot = -128783.047eV Step 38: Epot = -129592.649eV Ekin = 806.418eV Etot = -128786.231eV Step 39: Epot = -129647.119eV Ekin = 856.581eV Etot = -128790.538eV Step 40: Epot = -129665.002eV Ekin = 874.198eV Etot = -128790.804eV Step 41: Epot = -129654.542eV Ekin = 866.057eV Etot = -128788.484eV Step 42: Epot = -129655.266eV Ekin = 866.516eV Etot = -128788.749eV Step 43: Epot = -129663.942eV Ekin = 872.869eV Etot = -128791.073eV Step 44: Epot = -129646.117eV Ekin = 854.610eV Etot = -128791.506eV Step 45: Epot = -129596.400eV Ekin = 808.372eV Etot = -128788.028eV Step 46: Epot = -129561.757eV Ekin = 775.902eV Etot = -128785.856eV Step 47: Epot = -129579.735eV Ekin = 792.606eV Etot = -128787.129eV Step 48: Epot = -129629.309eV Ekin = 838.175eV Etot = -128791.134eV Step 49: Epot = -129659.307eV Ekin = 866.053eV Etot = -128793.255eV Step 50: Epot = -129655.002eV Ekin = 862.626eV Etot = -128792.376eV Step 51: Epot = -129648.746eV Ekin = 857.333eV Etot = -128791.413eV Step 52: Epot = -129657.228eV Ekin = 863.275eV Etot = -128793.953eV Step 53: Epot = -129653.428eV Ekin = 857.709eV Etot = -128795.719eV Step 54: Epot = -129613.325eV Ekin = 820.299eV Etot = -128793.026eV Step 55: Epot = -129569.882eV Ekin = 780.334eV Etot = -128789.548eV Step 56: Epot = -129574.259eV Ekin = 784.853eV Etot = -128789.406eV Step 57: Epot = -129623.452eV Ekin = 830.145eV Etot = -128793.307eV Step 58: Epot = -129666.217eV Ekin = 869.955eV Etot = -128796.262eV Step 59: Epot = -129668.508eV Ekin = 873.131eV Etot = -128795.378eV Step 60: Epot = -129653.026eV Ekin = 859.035eV Etot = -128793.991eV Step 61: Epot = -129653.227eV Ekin = 857.672eV Etot = -128795.556eV Step 62: Epot = -129657.065eV Ekin = 859.225eV Etot = -128797.840eV Step 63: Epot = -129631.260eV Ekin = 834.497eV Etot = -128796.763eV Step 64: Epot = -129586.275eV Ekin = 793.560eV Etot = -128792.715eV Step 65: Epot = -129572.147eV Ekin = 780.631eV Etot = -128791.516eV Step 66: Epot = -129605.296eV Ekin = 810.945eV Etot = -128794.351eV Step 67: Epot = -129649.955eV Ekin = 852.287eV Etot = -128797.668eV Step 68: Epot = -129664.583eV Ekin = 866.057eV Etot = -128798.526eV Step 69: Epot = -129651.364eV Ekin = 854.834eV Etot = -128796.529eV Step 70: Epot = -129645.825eV Ekin = 849.377eV Etot = -128796.448eV Step 71: Epot = -129651.242eV Ekin = 852.374eV Etot = -128798.868eV Step 72: Epot = -129635.424eV Ekin = 836.037eV Etot = -128799.387eV Step 73: Epot = -129593.856eV Ekin = 797.441eV Etot = -128796.415eV Step 74: Epot = -129569.291eV Ekin = 775.070eV Etot = -128794.220eV Step 75: Epot = -129592.963eV Ekin = 796.785eV Etot = -128796.177eV Step 76: Epot = -129641.187eV Ekin = 840.996eV Etot = -128800.191eV Step 77: Epot = -129666.154eV Ekin = 864.446eV Etot = -128801.708eV Step 78: Epot = -129655.084eV Ekin = 854.900eV Etot = -128800.185eV Step 79: Epot = -129642.137eV Ekin = 842.303eV Etot = -128799.834eV Step 80: Epot = -129644.443eV Ekin = 842.619eV Etot = -128801.824eV Step 81: Epot = -129636.401eV Ekin = 833.666eV Etot = -128802.735eV Step 82: Epot = -129604.452eV Ekin = 803.856eV Etot = -128800.596eV Step 83: Epot = -129575.009eV Ekin = 776.883eV Etot = -128798.126eV Step 84: Epot = -129583.019eV Ekin = 784.694eV Etot = -128798.325eV Step 85: Epot = -129622.924eV Ekin = 821.153eV Etot = -128801.771eV Step 86: Epot = -129655.369eV Ekin = 851.102eV Etot = -128804.268eV Step 87: Epot = -129655.577eV Ekin = 851.463eV Etot = -128804.115eV Step 88: Epot = -129644.464eV Ekin = 840.994eV Etot = -128803.470eV Step 89: Epot = -129644.259eV Ekin = 839.590eV Etot = -128804.668eV Solvent dynamic component Tinker terminated abnormally, cannot proceed. Launching AI2BMD with Docker: docker run -w /mnt/data2/home_data/ztliu/quantum --gpus all --rm -v /data2/home_data/ztliu/quantum:/mnt/data2/home_data/ztliu/quantum -v /data2/home_data/ztliu/quantum/chig_preprocessed:/mnt/data2/home_data/ztliu/quantum/chig_preprocessed ghcr.io/microsoft/ai2bmd:latest python -u /ai2bmd/main.py --prot-file /mnt/data2/home_data/ztliu/quantum/chig.pdb --preeq-steps 0 --sim-steps 1000 --record-per-steps 1 --base-dir /mnt/data2/home_data/ztliu/quantum

[Frank-LIU-520]

BTW, how can I set the tinker parameters in docker?

[Frank-LIU-520]

How can I set tinker-GPU to run this. I have tried the args '--gpus 4' but nothing happened. It is still running on cpu.

[ElwynWang]

The screen output says: ERROR:root:tinker-GPU is specified, but there's no GPU. Reverting back to CPU. You should check whether the GPU is available and works well. There's no need to set any parameters in Docker. In addition, make sure to the GPU type is in the support list (see README)

[Frank-LIU-520]

I have made the GPU available and worked well accoding to the README support list. However, this issue doesn't dispear. It can't sustain for too long in real case dynamics.

[ElwynWang]

Has the error output disappeared? If not, you device setting still has problems. Furthermore, I don't believe RTX 3090 you used is in the support list. As shown in the previous response, make sure to the GPU type is in the support list