[gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

[Tsjerk Wassenaar]

Hi,

So many posts and replies on a single issue, and still no exact
command lines, nor grompp output, nor gromacs version. Lin, please be
aware that such errors only make sense in the context of what you did.
You'll have to provide all information that might be related to it.
I'm pretty sure that your command lines will reveal the problem, and
otherwise the grompp output will.

If I have to make a guess, which is all one can do with the
information provided, I'd say the PBC is incorrect. Maybe you
converted to .pdb format at an intermediary step which is known to
remove the PBC in some gromacs versions.

Cheers,

Tsjerk

On Thu, Dec 31, 2009 at 2:47 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Chih-Ying Lin wrote:
>>
>>  Hi
>> what does the max max 597108032.000000 (between atoms 366 and 368) mean?
>> is it the max force or max length of the system?
>> where is the max force listed?
>
> Don't know.
>
>> max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000
>> bonds that rotated more than 30 degrees:
>> what does previous, current mean?
>> is it previous length and current length?
>
> Yeah probably. You need to understand what LINCS does to make some sense of
> this output.
>
> It doesn't really matter though. A well-behaved simulation will have none of
> these warnings. Atoms 366 and 368 are connected by a constraint and unhappy
> at the start of the simulation. In the output you quote, their distance has
> gone from under 1nm to a ridiculous number. Look at the region of those
> atoms in the starting configuration, and work out why. The most likely
> hypothesis is that some other atom is so close to them that they experienced
> a massive force, and had massive LJ.
>
> Mark
>
>> Thank you
>> Lin
>>    Step 0, time 0 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000
>> bonds that rotated more than 30 degrees:
>>  *atom 1 atom 2  angle  previous, current, constraint length
>> *     26     39   52.0    0.1530   0.1699      0.1530     39     40   69.4
>>    0.1230   0.1423      0.1230       39     41   40.7    0.1330   0.1502
>>  0.1330     75     76   36.0    0.1250   0.1252      0.1250        133
>>  134   69.5    0.1530   0.1937      0.1530
>>    134    135   89.8    0.1470   0.2036      0.1470
>>    344    346   42.4    0.1470   0.2090      0.1470
>>    346    347   42.2    0.1530   0.2141      0.1530
>>    346    359   63.9    0.1530 26006.0332      0.1530
>>    359    360   56.9    0.1230 26006.0469      0.1230
>>    359    361   83.2    0.1330 82898.5859      0.1330
>>    361    362   77.5    0.1000 82845.7109      0.1000
>>    361    363   83.8    0.1470 398710.1875      0.1470
>>    363    364   89.3    0.1530 1909291.8750      0.1530
>>    363    369   85.2    0.1530 393002.8125      0.1530
>>    364    365   90.0    0.1508 31146174.0000      0.1530
>>    365    366   90.2    0.1544 66925512.0000      0.1530
>>    366    367   92.7    0.1301 73689816.0000      0.1250
>>    366    368   87.0    0.1305 74638504.0000      0.1250
>>    369    370   72.1    0.1230 65978.3203      0.1230
>>    369    371   72.6    0.1330 66864.2812      0.1330
>>    371    372   85.7    0.1000 10685.0596      0.1000
>>    371    373   61.0    0.1470 10685.1035      0.1470      373    374
>> 33.3    0.1530   0.1896      0.1530
>>    373    377   33.5    0.1530   0.1933      0.1530
>>    547    548   90.1    0.1089   0.1358      0.1090
>>    898    900   89.9    0.1530   0.4741      0.1530
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist