Dear Gromacs users I am using amber99sb-ildn.ff force field for protein and I used GAFF for ligand parameterization. I tried different options e.g using constraint =all bonds as well as h-bonds. Reducing the time step to 1 fs but still, I could not solve the problem and get lincs warning production run as below:- Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035343, max 2.112628 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.0 2.2392 0.1552 0.1080 3770 3771 90.0 0.1045 0.1696 0.1090 3770 3772 90.0 2.9369 0.1212 0.1090 3770 3773 90.0 0.1043 0.3393 0.1090 Wrote pdb files with previous and current coordinates
Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035038, max 2.096736 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.0 2.2392 0.1540 0.1080 3770 3771 90.0 0.1045 0.1689 0.1090 3770 3772 90.0 2.9369 0.1198 0.1090 3770 3773 90.0 0.1043 0.3375 0.1090 I would really appreciate your help in fixing this problem I am facing since long. Thanks. Sadaf -- 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.