[gmx-users] LINCS warning

Vanessa Oklejas voklejas at stanford.edu
Sun Jul 2 23:28:41 CEST 2006


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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