Hello Saranya,This error means that during the nvt equilibrium high forces occurred that made it impossible to resolve the bond constraints. The very high forces occurred most likely are due to some high tension in the system. As indicated in the error message you can. Reduce the time step of your run initially to relax the structure first. Check the output PDB structure at the site where the error occurred (atoms 217 and 218), possibly removing or displacing the offending water molecule manually. Check that you used a well relaxed structure from energy minimisationBest, Christian -------- Original message --------From: saranya <saranyahone...@gmail.com> Date: 01/11/2019 07:48 (GMT+01:00) To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Hello everyone,while running nvt equilibration i am getting the error as:Step 12, time 0.024 (ps) LINCS WARNINGrelative constraint deviation after LINCS:rms nan, max 92522.640625 (between atoms 217 and 218)bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 277 278 58.9 0.1090 74.2482 0.1090 281 282 35.8 0.1098 73.5336 0.1090 281 283 119.3 0.1097 74.0780 0.1090 281 284 63.5 0.1097 74.2253 0.1090step 12: One or more water molecules can not be settled.Check for bad contacts and/or reduce the timestep if appropriate.Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1#Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1#Wrote pdb files with previous and current coordinatesSegmentation fault (core dumped)how can i resolve this error...?With Regards,*Saranya Vasudevan,**Research Scholar,**Molecular Quantum Mechanics Laboratory,**Department of Physics,**Bharathiar University,**Coimbatore-46*-- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list
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