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. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> 05/07/19, 09:58:23 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
