[gmx-users] LINCS error in MD simulation

[f vazifeshenas]

Thanks a lot for your guidance.
I was trying to Run this protein with ligand for 20ns and in first 11ns of
it i did get this LINCS error.



Step 5009957, time 10019.9 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000219, max 0.005436 (between atoms 2836 and 2835)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2836   2835   90.0    0.1236   0.1005      0.1000

------------------------------
-------------------------
Program gmx, VERSION 5.0.5
Source code file: /home/soft/gromacs-5.0.5/src/gromacs/mdlib/constr.c,
line: 224

Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


I have read the link and it referred to system blowing up.
How can i be assured  that my system is blown up? and if it is it right to
use "-append" in this condition?



On Sun, Apr 10, 2016 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/10/16 2:48 AM, f vazifeshenas wrote:
>
>> Dear all
>> Hi
>> I am trying to Run one protein with ligand and i am getting a note and an
>> error as fallows:
>>
>> Step 5009957, time 10019.9 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000219, max 0.005436 (between atoms 2836 and 2835)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>     2836   2835   90.0    0.1236   0.1005      0.1000
>>
>> -------------------------------------------------------
>> Program gmx, VERSION 5.0.5
>> Source code file: /home/soft/gromacs-5.0.5/src/gromacs/mdlib/constr.c,
>> line: 224
>>
>> Fatal error:
>> Too many LINCS warnings (1000)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> Does anybody know to deal with this LINCS error?
>>
>>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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