[gmx-users] LINCS Warning using mdrun

[Gaurav Chopra]

Hi

I get the following error when using mdrun for a protein in solution. I 
have checked the structure and everything looks fine to me. Could you 
suggested anything else I could do.

Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    898    899   41.6    0.1015   0.0997      0.1010
    898    900   38.1    0.1038   0.0984      0.1010
starting mdrun 'HEADER Output set 125 with rmsf= .982 of 
1nkd.cl_nH_tir.pdb in water'
100000 steps,    200.0 ps.


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:

Thanks
gaurav