GROMACS version: 2020.6
Hello gromacs users,
I have a complex of interactions between two proteins where there is clashes between structures. I used charmm-gui to generate files. I progressed to equilibration stage but production stage does not run.I get the following warning:
step 0
Step 12, time 0.048 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016073, max 0.987059 (between atoms 3778 and 3776)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3777 3776 90.0 0.1109 0.1429 0.1111
3778 3776 90.0 0.1110 0.2208 0.1111
7948 7949 90.0 0.0997 0.1747 0.0997
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 coordinates
Step 13, time 0.052 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 15.790467, max 1167.853760 (between atoms 7906 and 7909)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3769 3768 33.7 0.1099 0.1122 0.1111
3770 3768 34.0 0.1100 0.1103 0.1111
3777 3776 91.9 0.1429 37.3072 0.1111
3778 3776 153.3 0.2208 33.4928 0.1111
7906 7907 89.9 0.1111 0.8065 0.1111
7906 7908 90.0 0.1111 0.9185 0.1111
7906 7909 118.5 0.1111 129.8596 0.1111
7948 7949 90.0 0.1747 0.2635 0.0997
Back Off! I just backed up step13b.pdb to ./
Kindly help me, please
Thank you.