[gmx-users] LINCS Warning using mdrun

[Steffen Wolf]

Gaurav Chopra wrote:
> 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
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Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And 
have you run a minimization before starting the simulation?
hear from you soon
Steffen

-- 
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany