Dear All In doing umbrella sampling ,when I want to generate NPT every thing is going well but one error is occuring in the first. please let me know how can I solve this problem. Is it usefull to extend the degree which is defined in .mdp file? Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50000 steps, 100.0 ps.
Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 40.6 0.1143 0.1260 0.1140 5293 5294 82.7 0.1221 2613.7048 0.1090 5291 5293 77.2 0.1517 6084.3052 0.1390 5291 5292 101.0 0.1117 1519.0425 0.1090 5289 5291 87.7 0.1353 6893.7969 0.1390 5289 5290 88.4 0.1437 7531.5815 0.1360 5289 5287 88.4 0.1456 7542.5801 0.1390 5287 5288 89.7 0.1092 381.6111 0.1090 5285 5287 92.3 0.1395 355.0215 0.1390 5285 5286 123.8 0.1101 44.8588 0.1090 5284 5293 89.0 0.1478 4606.4570 0.1390 5284 5285 79.3 0.1402 173.6082 0.1390 5278 5279 78.9 0.1529 1.1246 0.1530 5277 5278 122.9 0.1545 13.1470 0.1530 5276 5284 84.9 0.1422 159.0514 0.1390 5276 5277 68.4 0.1543 90.8518 0.1530 5276 5275 39.5 0.1439 72.5391 0.1430 5274 5275 103.7 0.1436 21.6098 0.1430 5273 5274 108.6 0.1394 3.3410 0.1390 5276 5272 45.7 0.1402 80.7004 0.1390 5272 5273 127.3 0.1340 14.2414 0.1330 5272 5270 69.8 0.1336 12.6282 0.1330 5270 5271 113.3 0.1092 0.2532 0.1090 5268 5270 104.5 0.1391 0.2727 0.1390 5268 5269 44.0 0.1091 0.1624 0.1090 5273 5266 58.5 0.1342 14.0148 0.1330 5265 5268 36.7 0.1394 0.1774 0.1390 Actually md is crush,of course I think so. Thanks in advance -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
