[gmx-users] LINCS warning in md run

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi everybody,
during the mdrun_mpi I get many LINCS warnings like for example:

Step 1143, time 1.143 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.265373, max 1.416702 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    976    979   90.0    0.1072   0.2320      0.0960


But I don't know why. I already minimized my protein. And also in the
grompp run there were no error messages. This was the end of my grompp
output:


processing index file...
Making dummy/rest group for Acceleration containing 80212 elements
Making dummy/rest group for Freeze containing 51274 elements
Making dummy/rest group for VCM containing 80212 elements
Number of degrees of freedom in T-Coupling group System is 102623.00
Making dummy/rest group for User1 containing 80212 elements
Making dummy/rest group for User2 containing 80212 elements
Making dummy/rest group for XTC containing 80212 elements
Making dummy/rest group for Or. Res. Fit containing 80212 elements
Making dummy/rest group for QMMM containing 80212 elements
T-Coupling       has 1 element(s): System
Energy Mon.      has 2 element(s): Protein non-Protein
Acceleration     has 1 element(s): rest
Freeze           has 2 element(s): Protein_&_!TYP rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
Estimate for the relative computational load of the PME mesh part: 0.32
writing run input file...


Can you please help me?
Thank you,
 Eva