[gmx-users] NPT

[mohsen ramezanpour]

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