[gmx-users] LINCS error during mdrun

[Tsjerk Wassenaar]

Hi Shangwa Han,

First of all, there is no general conclusion regarding such error.
Second, the general conclusion is: your system contains severe errors,
which have not been resolved during energy minimization, if you
performed any, but you didn't mention it.

If you would have browsed the archive more thoroughly or had read the
posts of the last days, regarding non-standard residues, you would
have noticed that the problem has been met before.

Now, first of all, what residue do you have? Did you perform energy
minimization (vacuum and/or solvated)? Did energy minimization
converge? Did the potential energy after energy minimization seem
reasonable (well negative)? What atoms are causing the failure? I have
no idea to what the atom numbers correspond...

Maybe it's good to have read the following (and taking the advice)
when asking a question on this (or any) list:
http://catb.org/esr/faqs/smart-questions.html

Tsjerk


On 1/25/07, 한상화 <hansh at kangwon.ac.kr> wrote:
>
>
>
>
> 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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>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623