[gmx-users] Relative constraint deviation after LINCS:

[Mark Abraham]

Hi,

That looks like your system is unstable while equilibrating. You often need
to start more gently than your eventual simulation conditions. Have a look
at the trajectory for clues about a possible bad starting structure.

Mark

On Fri, 5 Jul 2019 at 06:31, Dilip.H.N <cy16f01.dilip at nitk.edu.in> wrote:

> Hi all,
> I am running a simulation of peptide and during the course of the
> simulation after some steps, the simulation gets canceled stating the
> following message:
>
> Step 1848418, time 3696.84 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000008, max 0.000547 (between atoms 5577 and 5578)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    5577   5578   47.6    0.1111   0.1110      0.1111
>
> Step 1848419, time 3696.84 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000017, max 0.001112 (between atoms 5577 and 5580)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    5577   5578   39.9    0.1110   0.1111      0.1111
>
> Step 1848420, time 3696.84 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000024, max 0.001800 (between atoms 5577 and 5580)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    5577   5578   30.2    0.1111   0.1111      0.1111
>
> Step 1848421, time 3696.84 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000034, max 0.002419 (between atoms 5577 and 5580)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> /var/spool/slurmd/job29017/slurm_script: line 11: 91791 Segmentation fault
> gmx_mpi_d mdrun -v -s nvtmdd.tpr -deffnm nvtmdd
>
> Why is this happening..??
>
> Any suggestions on how can i resolve this issue..?
>
> Thank you.
> ---
> With Best Regards,
>
> Dilip.H.N
> Ph.D. Student.
>
>
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> 05/07/19,
> 09:58:23
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