GROMACS version: 2019.4
GROMACS modification: Yes/No
Dear Gromacs users,
I simulated the Protein-ligand complex. When I run NVT simulation with t-coupling = V-rescale, there is no error. But when I used the t-coupling = Nose-Hoover, error occurred below:
…
Step 2161, time 4.322 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.301654, max 14.453189 (between atoms 3935 and 3936)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3871 3872 69.0 0.1630 0.1171 0.1111
3871 3873 77.3 0.9858 0.1127 0.1111
3916 3917 90.0 0.0997 0.2134 0.0997
3933 3934 32.9 0.0997 0.0997 0.0997
3935 3936 90.0 3.0620 1.6689 0.1080
3941 3943 64.0 0.1108 0.1116 0.1111
Wrote pdb files with previous and current coordinates
Step 2162, time 4.324 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.464865, max 70.247780 (between atoms 3935 and 3936)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3871 3873 90.0 0.1172 0.6335 0.1111
3916 3917 90.0 0.2219 0.1085 0.0997
3933 3934 55.6 0.1037 0.0997 0.0997
3935 3936 90.0 1.7358 7.6948 0.1080
3941 3943 65.5 0.1160 0.1112 0.1111
Wrote pdb files with previous and current coordinates
Step 2163, time 4.326 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 2.634528, max 125.905602 (between atoms 3916 and 3917)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3871 3872 90.0 0.1118 0.1570 0.1111
3871 3873 64.9 0.6335 0.1071 0.1111
3916 3917 145.2 0.1085 12.6525 0.0997
3933 3934 47.7 0.0997 0.0997 0.0997
3935 3936 90.0 7.6948 1.5598 0.1080
3941 3943 67.7 0.1112 0.1108 0.1111
step 2163: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate
When I tried to find whether there is clash in system with using chimera ‘Find Clashes/Contacts’, there are no contact.
But I found that the error-occuring atoms are hydrogens and its neighbors.
Any advice on this would be greatly appreciated, thanks!