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 <[email protected]> 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. > > > [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 [email protected]. > -- 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 [email protected].
