[gmx-users] Relative constraint deviation after LINCS:

[Dilip.H.N]

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