Hi everyone,
I'm having trouble with performing 1 ns simulations on a 318 residue
long protein with 'mdrun'. The run.log file, included at the end of
this message, gives a 'LINCS warning' within a minute or two after
the simulation begins:
Step 148, time 0.296 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.151505 (between atoms 4353 and 4355) rms 0.002175
bonds that rotated more than 60 degrees:
I've have been minimizing the structure of the protein prior to
trying to perform the simulation (no problems here). Also, when I use
'grompp' to produce a .tpr file for a 1 ns MD simulation with the
minimized structure, I have no problems with this either. The .mdp
file that is fed into the .tpr file will work with different protein
structures (single residue mutants) without incident. So, it would
appear that the .mdp file used to compile the .tpr file is working.
What is really puzzling to me is that the simulation will sometimes
run properly and sometimes it won't even though it would appear
that I use the exact same .gro file. Does this sound familiar to anyone?
Thanks,
Vanessa
Reading file 1_T114A_F.tpr, VERSION 3.1.4 (single precision)
Reading file 1_T114A_F.tpr, VERSION 3.1.4 (single precision)
starting mdrun 'hALDR2 (060425 pH=6.5) w/ F inhibitor implicit water'
500000 steps, 1000.0 ps.
Step 148, time 0.296 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.151505 (between atoms 4353 and 4355) rms 0.002175
bonds that rotated more than 60 degrees:
bonds that rotated more than 60 degrees:
atom 1 atom 2 angle previous, current, constraint length
4353 4355 90.3 0.1010 0.1163 0.1010
Step 148, time 0.296 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.150984 (between atoms 4353 and 4355) rms 0.002227
bonds that rotated more than 60 degrees:
atom 1 atom 2 angle previous, current, constraint length
4353 4355 90.0 0.1010 0.1162 0.1010
Step 149, time 0.298 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.053408 (between atoms 4353 and 4355) rms 0.000836
bonds that rotated more than 60 degrees:
atom 1 atom 2 angle previous, current, constraint length
4353 4355 89.6 0.1162 0.1064 0.1010
Step 149, time 0.298 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.049700 (between atoms 4353 and 4355) rms 0.000769
bonds that rotated more than 60 degrees:
atom 1 atom 2 angle previous, current, constraint length
atom 1 atom 2 angle previous, current, constraint length
4353 4355 90.0 0.1162 0.1060 0.1010
Step 150, time 0.3 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 166995.593750 (between atoms 4348 and 4350) rms 3256.995850
bonds that rotated more than 60 degrees:
atom 1 atom 2 angle previous, current, constraint length
4329 4331 65.3 0.1449 2.0483 0.1449
4331 4332 75.6 0.1090 2.0105 0.1090
4331 4333 64.6 0.1526 2.0440 0.1526
4331 4342 68.6 0.1522 9.4604 0.1522
4342 4343 68.4 0.1229 9.5175 0.1229
4342 4344 74.8 0.1335 33.8721 0.1335
4344 4345 79.4 0.1010 31.1369 0.1010
4344 4346 85.9 0.1450 170.9566 0.1449
4346 4347 86.5 0.1090 151.5872 0.1090
4346 4348 88.9 0.1527 774.3875 0.1526
4346 4356 84.6 0.1523 164.2752 0.1522
4348 4349 89.5 0.1091 647.3028 0.1090
4348 4350 90.0 0.1092 18202.6279 0.1090
4348 4351 89.7 0.1527 957.9619 0.1522
4351 4352 89.6 0.1234 262.4561 0.1229
4351 4352 89.6 0.1234 262.4561 0.1229
4351 4353 90.5 0.1355 1149.1741 0.1335
4353 4354 89.7 0.1007 178.1642 0.1010
4353 4355 90.0 0.1060 16749.2714 0.1010
4356 4357 76.1 0.1229 38.4753 0.1229
4356 4358 73.1 0.1335 39.2402 0.1335
4358 4359 69.5 0.1010 9.6261 0.1010
4358 4360 69.7 0.1449 10.2906 0.1449
4360 4361 72.9 0.1090 2.6064 0.1090
4360 4362 69.1 0.1526 2.6707 0.1526
4360 4376 63.9 0.1522 2.6586 0.1522
Wrote pdb files with previous and current coordinates
Step 150, time 0.3 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 166882.437500 (between atoms 4348 and 4350) rms 3256.037109
bonds that rotated more than 60 degrees:
atom 1 atom 2 angle previous, current, constraint length
4319 4321 77.0 0.1449 0.2666 0.1449
4321 4322 78.4 0.1090 0.1816 0.1090
4321 4323 72.4 0.1526 0.2694 0.1526
4321 4327 69.1 0.1522 0.3681 0.1522
4327 4328 73.5 0.1229 0.4389 0.1229
4327 4328 73.5 0.1229 0.4389 0.1229
4327 4329 80.0 0.1335 1.6753 0.1335
4329 4330 80.9 0.1010 1.3435 0.1010
4329 4331 85.1 0.1449 6.8655 0.1449
4331 4332 86.0 0.1090 6.3950 0.1090
4331 4333 85.4 0.1526 6.7474 0.1526
4331 4342 83.6 0.1522 12.4837 0.1522
4333 4334 85.9 0.1090 1.9833 0.1090
4333 4335 86.7 0.1090 2.0395 0.1090
4333 4336 86.6 0.1526 2.2687 0.1526
4336 4337 83.9 0.1090 0.3444 0.1090
4336 4338 84.0 0.1090 0.3467 0.1090
4336 4339 84.6 0.1522 0.4014 0.1522
4342 4343 85.2 0.1229 13.9188 0.1229
4342 4344 87.7 0.1335 43.2216 0.1335
4344 4345 88.3 0.1010 33.7636 0.1010
4344 4346 89.4 0.1450 183.1574 0.1449
4346 4347 89.5 0.1090 148.2331 0.1090
4346 4348 89.9 0.1527 761.9371 0.1526
4346 4356 89.1 0.1523 173.7133 0.1522
4348 4349 90.0 0.1091 635.9145 0.1090
4348 4350 90.0 0.1092 18190.2945 0.1090
4348 4351 89.9 0.1527 957.4889 0.1522
4351 4352 90.2 0.1234 269.4506 0.1229
4351 4353 90.0 0.1355 1155.7604 0.1335
4353 4354 89.9 0.1007 184.5258 0.1010
4353 4355 90.0 0.1060 16750.9137 0.1010
4356 4357 87.7 0.1229 41.7205 0.1229
4356 4358 87.4 0.1335 47.5530 0.1335
4358 4359 86.5 0.1010 15.9261 0.1010
4358 4360 86.5 0.1449 21.9933 0.1449
4360 4361 86.1 0.1090 7.3294 0.1090
4360 4362 86.1 0.1526 8.5779 0.1526
4360 4376 84.4 0.1522 8.0426 0.1522
4362 4363 84.4 0.1090 1.9181 0.1090
4362 4364 85.9 0.1090 2.0397 0.1090
4362 4365 84.0 0.1510 2.1297 0.1510
4365 4366 75.9 0.1400 0.3953 0.1400
4365 4374 75.3 0.1400 0.3941 0.1400
4366 4367 73.7 0.1080 0.1714 0.1080
4366 4368 60.9 0.1400 0.2290 0.1400
4372 4374 63.6 0.1400 0.2338 0.1400
4374 4375 68.7 0.1080 0.1679 0.1080
4376 4377 78.9 0.1229 1.8364 0.1229
4376 4378 78.4 0.1335 2.0470 0.1335
4378 4379 79.1 0.1010 0.5990 0.1010
4378 4380 80.6 0.1449 0.8133 0.1449
4380 4381 79.4 0.1090 0.1932 0.1090
4380 4382 82.3 0.1526 0.2756 0.1526
4380 4398 80.8 0.1522 0.2713 0.1522
Back Off! I just backed up step149.pdb to ./#step149.pdb.1#
Back Off! I just backed up step150.pdb to ./#step150.pdb.1#
Wrote pdb files with previous and current coordinates
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