[gmx-users] (no subject)

[Mark Abraham]

黄永棋 wrote:
> Hi
>  
>   I was trying to do a protein simulation with the protein embedded in a 
> dopc bilayer , but the mdrun killed with a message like this:
>  
> "  Step 124772, time 249.544 (ps)  LINCS WARNING
>    relative constraint deviation after LINCS:
>    max 78.497551 (between atoms 28341 and 28343) rms 0.598885
>    bonds that rotated more than 30 degrees:
>    atom 1 atom 2  angle  previous, current, constraint length
>    28332  28333  170.9    0.1000   0.9127      0.1000
>    28335  28336   30.4    0.1000   0.7634      0.1000
>    28335  28337  179.8    0.1000   6.4688      0.1000
>    28341  28342  140.6    0.1000   0.7312      0.1000
>    28341  28343  179.7    0.1000   7.9498      0.1000
>    Constraint error in algorithm Lincs at step 124772
>    Wrote pdb files with previous and current coordinates
> 
>    Segmentation fault  "
>  
>  
> I checked the gro. file and found these are water molucules . Can 
> anybody tell me why this  happened and what  shall I do to aviod this ?

Searching the mailing list for "LINCS WARNING" or similar would have
found the other ten thousand posts where people have been advised to
minimise their system better before equilibrating, or equilibrate better
before simulating, as well as suggestions that you describe your system
preparation methodology so that we don't have to read your mind.

Mark