Dear GROMACS users,
I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max 236965036032.000000 (between atoms 261 and 262) rms 7344678400.000000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 250 252 70.2 0.1331 0.0388 0.1330 252 253 133.7 0.1000 0.1070 0.1000 252 254 113.7 0.1471 584679.3560 0.1470 254 255 99.1 0.1531 4371462.3199 0.1530 254 268 113.2 0.1531 584679.3412 0.1530 255 256 104.0 0.1531 14918575.9155 0.1530 256 257 94.1 0.1391 71642892.3147 0.1390 256 259 118.9 0.1391 9989150.8212 0.1390 257 258 94.7 0.1090 53680649.8250 0.1090 257 261 92.0 0.1391 165281594.0708 0.1390 259 260 167.3 0.1090 3058365.4015 0.1090 259 263 102.7 0.1391 23632615.9567 0.1390 261 262 90.0 0.1090 25829189100.6878 0.1090 261 265 93.5 0.1391 151539192.8914 0.1390 263 264 102.7 0.1090 23369011.4797 0.1090 263 265 99.0 0.1391 51420376.9215 0.1390 265 266 96.0 0.1361 61029666.4858 0.1360 266 267 93.3 0.1000 22670607.4602 0.1000 268 269 123.5 0.1230 0.1132 0.1230 268 270 89.0 0.1331 0.0916 0.1330 270 271 32.2 0.1000 0.1280 0.1000 270 272 32.3 0.1471 0.1820 0.1470 I looked up the mailing list and found discussion about this subject but there appears to be no conclusions. Any suggestions would be greatly appreciated. Sanghwa Han
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