[gmx-users] LINCS error during mdrun

[한상화]

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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